Starting phenix.real_space_refine on Thu Feb 22 22:09:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7veb_31945/02_2024/7veb_31945_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7veb_31945/02_2024/7veb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7veb_31945/02_2024/7veb_31945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7veb_31945/02_2024/7veb_31945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7veb_31945/02_2024/7veb_31945_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7veb_31945/02_2024/7veb_31945_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'MEN:plan-2': 1, 'ASP:plan': 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, 'GLN:plan1': 1, 'ASP:plan': 2} 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: {'MEN:plan-2': 1, 'GLN:plan1': 1, 'ASP:plan': 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: {'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} 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: {'HIS:plan': 2, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6} 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: 18.87, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 15.00 Conformation dependent library (CDL) restraints added in 6.4 seconds 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 248 helices and 2 sheets defined 71.9% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.84 Creating SS restraints... Processing helix chain 'A' and resid 4 through 14 Processing helix chain 'A' and resid 21 through 46 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) Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 78 through 101 removed outlier: 3.591A pdb=" N VAL A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 126 through 139 Processing helix chain 'A' and resid 146 through 173 Processing helix chain 'B' and resid 4 through 15 Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 34 through 62 removed outlier: 3.521A pdb=" N ASN B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 79 through 101 Processing helix chain 'B' and resid 105 through 108 No H-bonds generated for 'chain 'B' and resid 105 through 108' Processing helix chain 'B' and resid 116 through 122 Processing helix chain 'B' and resid 126 through 144 Processing helix chain 'B' and resid 156 through 173 Processing helix chain 'C' and resid 4 through 15 removed outlier: 3.690A pdb=" N GLN C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 46 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 48 through 62 Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 78 through 101 Processing helix chain 'C' and resid 105 through 110 Processing helix chain 'C' and resid 115 through 121 Processing helix chain 'C' and resid 126 through 139 removed outlier: 3.521A pdb=" N LEU C 133 " --> pdb=" O TYR C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 173 Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 21 through 32 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 48 through 62 Processing helix chain 'D' and resid 64 through 67 No H-bonds generated for 'chain 'D' and resid 64 through 67' Processing helix chain 'D' and resid 79 through 101 Processing helix chain 'D' and resid 105 through 110 removed outlier: 3.553A pdb=" N ARG D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 122 Processing helix chain 'D' and resid 126 through 145 Processing helix chain 'D' and resid 156 through 173 Processing helix chain 'E' and resid 4 through 15 removed outlier: 3.807A pdb=" N GLN E 15 " --> pdb=" O ALA E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 46 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 48 through 62 Processing helix chain 'E' and resid 64 through 67 Processing helix chain 'E' and resid 78 through 101 Processing helix chain 'E' and resid 105 through 110 Processing helix chain 'E' and resid 115 through 121 Processing helix chain 'E' and resid 126 through 139 Processing helix chain 'E' and resid 146 through 173 removed outlier: 3.509A pdb=" N VAL E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 15 Processing helix chain 'F' and resid 21 through 32 Processing helix chain 'F' and resid 34 through 46 Processing helix chain 'F' and resid 48 through 62 Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 79 through 101 Processing helix chain 'F' and resid 105 through 109 Processing helix chain 'F' and resid 115 through 122 Processing helix chain 'F' and resid 126 through 145 Processing helix chain 'F' and resid 156 through 173 Processing helix chain 'G' and resid 4 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 21 through 46 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 48 through 62 Processing helix chain 'G' and resid 64 through 67 Processing helix chain 'G' and resid 78 through 101 Processing helix chain 'G' and resid 105 through 110 Processing helix chain 'G' and resid 115 through 121 Processing helix chain 'G' and resid 126 through 139 Processing helix chain 'G' and resid 146 through 173 Processing helix chain 'H' and resid 4 through 15 Processing helix chain 'H' and resid 21 through 32 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 48 through 62 Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 79 through 101 removed outlier: 3.552A pdb=" N ILE H 91 " --> pdb=" O ASP H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 110 Processing helix chain 'H' and resid 115 through 122 Processing helix chain 'H' and resid 126 through 144 Processing helix chain 'H' and resid 156 through 173 Processing helix chain 'I' and resid 4 through 15 removed outlier: 3.650A pdb=" N GLN I 15 " --> pdb=" O ALA I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 46 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) Processing helix chain 'I' and resid 48 through 62 Processing helix chain 'I' and resid 64 through 67 Processing helix chain 'I' and resid 78 through 101 removed outlier: 3.724A pdb=" N GLY I 89 " --> pdb=" O ALA I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 110 Processing helix chain 'I' and resid 115 through 121 removed outlier: 3.535A pdb=" N SER I 120 " --> pdb=" O SER I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 139 Processing helix chain 'I' and resid 146 through 173 Processing helix chain 'J' and resid 4 through 15 Processing helix chain 'J' and resid 21 through 32 Processing helix chain 'J' and resid 34 through 46 Processing helix chain 'J' and resid 48 through 62 Processing helix chain 'J' and resid 64 through 66 No H-bonds generated for 'chain 'J' and resid 64 through 66' Processing helix chain 'J' and resid 79 through 101 Processing helix chain 'J' and resid 105 through 109 Processing helix chain 'J' and resid 115 through 122 Processing helix chain 'J' and resid 126 through 145 Processing helix chain 'J' and resid 156 through 173 Processing helix chain 'K' and resid 4 through 14 Processing helix chain 'K' and resid 21 through 46 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 48 through 62 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 67 Processing helix chain 'K' and resid 78 through 101 Processing helix chain 'K' and resid 105 through 110 Processing helix chain 'K' and resid 115 through 121 Processing helix chain 'K' and resid 126 through 138 Processing helix chain 'K' and resid 146 through 173 Processing helix chain 'L' and resid 4 through 15 removed outlier: 3.657A pdb=" N ARG L 15 " --> pdb=" O GLN L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 32 Processing helix chain 'L' and resid 34 through 46 Processing helix chain 'L' and resid 48 through 62 Processing helix chain 'L' and resid 79 through 101 removed outlier: 3.884A pdb=" N ILE L 91 " --> pdb=" O ASP L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 110 Processing helix chain 'L' and resid 115 through 122 Processing helix chain 'L' and resid 126 through 145 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 156 through 173 Processing helix chain 'M' and resid 4 through 14 Processing helix chain 'M' and resid 21 through 46 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) Processing helix chain 'M' and resid 48 through 62 Processing helix chain 'M' and resid 64 through 67 Processing helix chain 'M' and resid 78 through 101 Processing helix chain 'M' and resid 105 through 110 Processing helix chain 'M' and resid 115 through 121 Processing helix chain 'M' and resid 126 through 138 Processing helix chain 'M' and resid 146 through 173 Processing helix chain 'N' and resid 4 through 15 Processing helix chain 'N' and resid 21 through 32 Processing helix chain 'N' and resid 34 through 62 removed outlier: 3.628A pdb=" N ASN N 47 " --> pdb=" O ARG N 43 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER N 49 " --> pdb=" O THR N 45 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR N 50 " --> pdb=" O SER N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 66 No H-bonds generated for 'chain 'N' and resid 64 through 66' Processing helix chain 'N' and resid 79 through 101 Processing helix chain 'N' and resid 105 through 109 Processing helix chain 'N' and resid 116 through 122 Processing helix chain 'N' and resid 126 through 144 Processing helix chain 'N' and resid 156 through 173 Processing helix chain 'O' and resid 4 through 14 Processing helix chain 'O' and resid 21 through 46 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 48 through 62 Processing helix chain 'O' and resid 64 through 67 Processing helix chain 'O' and resid 78 through 101 Processing helix chain 'O' and resid 105 through 110 Processing helix chain 'O' and resid 115 through 122 Processing helix chain 'O' and resid 126 through 139 Processing helix chain 'O' and resid 147 through 173 Processing helix chain 'P' and resid 4 through 15 Processing helix chain 'P' and resid 21 through 32 Processing helix chain 'P' and resid 34 through 46 Processing helix chain 'P' and resid 48 through 62 Processing helix chain 'P' and resid 64 through 66 No H-bonds generated for 'chain 'P' and resid 64 through 66' Processing helix chain 'P' and resid 79 through 101 Processing helix chain 'P' and resid 105 through 110 Processing helix chain 'P' and resid 115 through 122 Processing helix chain 'P' and resid 126 through 145 Processing helix chain 'P' and resid 156 through 173 Processing helix chain 'Q' and resid 4 through 15 removed outlier: 3.955A pdb=" N GLN Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 46 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) Processing helix chain 'Q' and resid 50 through 62 Processing helix chain 'Q' and resid 64 through 66 No H-bonds generated for 'chain 'Q' and resid 64 through 66' Processing helix chain 'Q' and resid 78 through 101 Processing helix chain 'Q' and resid 105 through 110 Processing helix chain 'Q' and resid 115 through 121 Processing helix chain 'Q' and resid 126 through 139 Processing helix chain 'Q' and resid 146 through 173 removed outlier: 3.607A pdb=" N ASP Q 167 " --> pdb=" O ASN Q 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 15 Processing helix chain 'R' and resid 21 through 32 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 34 through 46 Processing helix chain 'R' and resid 48 through 62 Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'R' and resid 79 through 101 Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'R' and resid 115 through 122 Processing helix chain 'R' and resid 126 through 145 Processing helix chain 'R' and resid 156 through 173 Processing helix chain 'S' and resid 4 through 14 Processing helix chain 'S' and resid 21 through 46 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 48 through 62 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 68 Processing helix chain 'S' and resid 78 through 101 Processing helix chain 'S' and resid 105 through 110 Processing helix chain 'S' and resid 115 through 121 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 126 through 139 Processing helix chain 'S' and resid 146 through 173 Processing helix chain 'T' and resid 4 through 15 Processing helix chain 'T' and resid 21 through 32 Processing helix chain 'T' and resid 34 through 46 Processing helix chain 'T' and resid 48 through 62 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 64 through 67 No H-bonds generated for 'chain 'T' and resid 64 through 67' Processing helix chain 'T' and resid 78 through 101 Processing helix chain 'T' and resid 105 through 109 Processing helix chain 'T' and resid 115 through 122 Processing helix chain 'T' and resid 126 through 144 Processing helix chain 'T' and resid 156 through 173 Processing helix chain 'U' and resid 4 through 14 Processing helix chain 'U' and resid 21 through 46 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 48 through 62 Processing helix chain 'U' and resid 64 through 67 Processing helix chain 'U' and resid 78 through 101 Processing helix chain 'U' and resid 105 through 110 Processing helix chain 'U' and resid 115 through 121 Processing helix chain 'U' and resid 126 through 139 Processing helix chain 'U' and resid 147 through 173 Processing helix chain 'V' and resid 4 through 15 Processing helix chain 'V' and resid 21 through 32 Processing helix chain 'V' and resid 34 through 46 Processing helix chain 'V' and resid 48 through 62 Processing helix chain 'V' and resid 64 through 66 No H-bonds generated for 'chain 'V' and resid 64 through 66' Processing helix chain 'V' and resid 80 through 101 Processing helix chain 'V' and resid 105 through 109 Processing helix chain 'V' and resid 115 through 122 removed outlier: 3.553A pdb=" N GLN V 120 " --> pdb=" O ARG V 116 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 145 Processing helix chain 'V' and resid 156 through 173 Processing helix chain 'W' and resid 4 through 15 removed outlier: 3.662A pdb=" N GLN W 15 " --> pdb=" O ALA W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 46 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 48 through 62 Processing helix chain 'W' and resid 64 through 68 Processing helix chain 'W' and resid 78 through 101 removed outlier: 3.515A pdb=" N TYR W 97 " --> pdb=" O ARG W 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 105 through 110 Processing helix chain 'W' and resid 115 through 121 Processing helix chain 'W' and resid 126 through 139 Processing helix chain 'W' and resid 146 through 173 Processing helix chain 'X' and resid 4 through 15 Processing helix chain 'X' and resid 21 through 32 Processing helix chain 'X' and resid 34 through 62 removed outlier: 5.525A pdb=" N SER X 49 " --> pdb=" O THR X 45 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR X 50 " --> pdb=" O SER X 46 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 66 No H-bonds generated for 'chain 'X' and resid 64 through 66' Processing helix chain 'X' and resid 77 through 101 Processing helix chain 'X' and resid 105 through 110 Processing helix chain 'X' and resid 115 through 122 Processing helix chain 'X' and resid 126 through 144 Processing helix chain 'X' and resid 156 through 173 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) Processing helix chain 'Y' and resid 55 through 65 Processing helix chain 'Z' and resid 31 through 43 Processing helix chain 'Z' and resid 51 through 53 No H-bonds generated for 'chain 'Z' and resid 51 through 53' Processing helix chain 'Z' and resid 56 through 64 removed outlier: 3.553A pdb=" N LEU Z 61 " --> pdb=" O SER Z 57 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 78 Processing helix chain 'Z' and resid 80 through 85 removed outlier: 3.646A pdb=" N LYS Z 85 " --> pdb=" O LEU Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 103 Processing helix chain 'Z' and resid 111 through 123 Processing helix chain 'Z' and resid 126 through 135 Processing helix chain 'Z' and resid 137 through 142 Processing helix chain 'Z' and resid 162 through 171 Processing helix chain 'Z' and resid 192 through 196 removed outlier: 3.679A pdb=" N THR Z 196 " --> pdb=" O ARG Z 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 192 through 196' Processing helix chain 'Z' and resid 218 through 220 No H-bonds generated for 'chain 'Z' and resid 218 through 220' Processing helix chain 'Z' and resid 264 through 277 removed outlier: 4.624A pdb=" N SER Z 268 " --> pdb=" O GLU Z 265 " (cutoff:3.500A) Processing helix chain 'a' and resid 39 through 53 removed outlier: 3.572A pdb=" N GLU a 44 " --> pdb=" O SER a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 66 through 73 removed outlier: 3.725A pdb=" N ALA a 73 " --> pdb=" O GLU a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 88 Processing helix chain 'a' and resid 90 through 95 Processing helix chain 'a' and resid 102 through 112 removed outlier: 3.740A pdb=" N GLU a 107 " --> pdb=" O TYR a 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 134 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 136 through 144 Processing helix chain 'a' and resid 147 through 153 Processing helix chain 'a' and resid 170 through 173 No H-bonds generated for 'chain 'a' and resid 170 through 173' Processing helix chain 'a' and resid 181 through 184 Processing sheet with id= A, 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= B, first strand: chain 'Z' and resid 258 through 263 2240 hydrogen bonds defined for protein. 6626 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: 12.47 Time building geometry restraints manager: 16.06 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: 74.34 - 91.49: 2 91.49 - 108.64: 1460 108.64 - 125.79: 46881 125.79 - 142.94: 899 142.94 - 160.09: 1 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: 1159 2.71 - 3.26: 39809 3.26 - 3.81: 63554 3.81 - 4.35: 76086 4.35 - 4.90: 122292 Nonbonded interactions: 302900 Sorted by model distance: nonbonded pdb=" OG1 THR Z 156 " pdb=" OB CYC L 201 " model vdw 2.165 2.440 nonbonded pdb=" OH TYR R 76 " pdb=" NH2 ARG S 93 " model vdw 2.229 2.520 nonbonded pdb=" NH1 ARG B 79 " pdb=" O ASN Y 30 " model vdw 2.244 2.520 nonbonded pdb=" O TYR R 76 " pdb=" OG1 THR R 77 " model vdw 2.279 2.440 nonbonded pdb=" O TYR L 76 " pdb=" OG1 THR L 77 " model vdw 2.284 2.440 ... (remaining 302895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 174 or resid 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 174 or resid \ 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 174 or resid \ 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 174 or resid \ 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 174 or resid \ 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 174 or resid \ 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 174 or resid \ 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 174 or resid \ 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 174 or resid \ 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 \ 174 or resid 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 174 or resid \ 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 174 or resid 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 174 or resid \ 201 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 174 or resid 201 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 174 or resid \ 201 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 174 or resid 201 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 174 or resid \ 201 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 174 or resid \ 201 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 174 or resid \ 201 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 174 or resid \ 201 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 174 or resid \ 201 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 174 or resid 201 through 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 174 or resid 201 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 174 or resid 201 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.340 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 93.070 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.550 ------------------------------------------------------------------------------- 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= 0.746 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 : 8.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (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 TRP 0.014 0.002 TRP C 128 HIS 0.005 0.001 HIS G 140 PHE 0.020 0.002 PHE a 82 TYR 0.021 0.001 TYR D 76 ARG 0.009 0.000 ARG R 86 *********************** 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 fitting. rotamer outliers: 25 poor density : 2170 time to evaluate : 4.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.9022 (t70) cc_final: 0.8545 (t70) REVERT: A 17 ARG cc_start: 0.8503 (ptp-170) cc_final: 0.7653 (ptp-110) REVERT: A 18 PHE cc_start: 0.8095 (m-80) cc_final: 0.7338 (m-80) REVERT: A 33 ARG cc_start: 0.9176 (mmm160) cc_final: 0.8804 (tpt170) REVERT: A 38 MET cc_start: 0.9117 (mmt) cc_final: 0.8211 (tmm) REVERT: A 39 GLU cc_start: 0.9641 (tp30) cc_final: 0.9101 (mm-30) REVERT: A 49 GLN cc_start: 0.9268 (tp40) cc_final: 0.9026 (tp-100) REVERT: A 63 PHE cc_start: 0.9009 (m-80) cc_final: 0.8632 (m-10) REVERT: A 87 ASP cc_start: 0.9161 (m-30) cc_final: 0.8885 (m-30) REVERT: A 90 TYR cc_start: 0.9265 (m-10) cc_final: 0.8940 (m-80) REVERT: A 91 TYR cc_start: 0.9053 (m-80) cc_final: 0.8837 (m-10) REVERT: A 122 PHE cc_start: 0.8741 (m-80) cc_final: 0.8385 (m-10) REVERT: A 124 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8939 (mp) REVERT: A 166 ILE cc_start: 0.9772 (mt) cc_final: 0.9450 (mm) REVERT: A 167 ASP cc_start: 0.9188 (t0) cc_final: 0.8560 (t0) REVERT: A 170 ILE cc_start: 0.9391 (mt) cc_final: 0.9029 (mt) REVERT: B 27 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9141 (mm) REVERT: B 29 ASN cc_start: 0.8286 (m-40) cc_final: 0.8054 (t0) REVERT: B 32 LYS cc_start: 0.9038 (ttpp) cc_final: 0.8645 (tppt) REVERT: B 33 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8846 (mm-30) REVERT: B 49 SER cc_start: 0.9630 (m) cc_final: 0.9297 (p) REVERT: B 67 ILE cc_start: 0.9362 (pt) cc_final: 0.9137 (mm) REVERT: B 89 GLU cc_start: 0.9563 (pt0) cc_final: 0.9332 (tt0) REVERT: B 93 ARG cc_start: 0.9481 (ttp80) cc_final: 0.8957 (mtp180) REVERT: B 112 LEU cc_start: 0.9343 (mt) cc_final: 0.8975 (mp) REVERT: B 119 TYR cc_start: 0.9330 (m-80) cc_final: 0.8750 (m-80) REVERT: B 120 GLN cc_start: 0.8762 (mt0) cc_final: 0.8177 (tm-30) REVERT: B 129 VAL cc_start: 0.9721 (t) cc_final: 0.9520 (t) REVERT: B 145 ASN cc_start: 0.9248 (t0) cc_final: 0.8692 (p0) REVERT: C 3 THR cc_start: 0.8823 (m) cc_final: 0.8494 (p) REVERT: C 20 SER cc_start: 0.9369 (p) cc_final: 0.9126 (p) REVERT: C 31 PHE cc_start: 0.9400 (m-80) cc_final: 0.9117 (m-80) REVERT: C 65 TYR cc_start: 0.7492 (p90) cc_final: 0.7197 (p90) REVERT: C 69 MET cc_start: 0.7416 (ttm) cc_final: 0.6750 (ttm) REVERT: C 87 ASP cc_start: 0.9692 (m-30) cc_final: 0.9475 (m-30) REVERT: C 94 MET cc_start: 0.9533 (mmt) cc_final: 0.9142 (mmm) REVERT: C 122 PHE cc_start: 0.9067 (m-10) cc_final: 0.8837 (m-10) REVERT: C 125 SER cc_start: 0.9513 (t) cc_final: 0.9137 (p) REVERT: C 128 TRP cc_start: 0.8340 (m-10) cc_final: 0.8075 (m-10) REVERT: D 13 ASP cc_start: 0.8701 (t70) cc_final: 0.8417 (t0) REVERT: D 24 PHE cc_start: 0.8362 (m-80) cc_final: 0.8064 (m-80) REVERT: D 32 LYS cc_start: 0.9418 (ptmt) cc_final: 0.9145 (pttt) REVERT: D 46 SER cc_start: 0.8931 (m) cc_final: 0.8686 (m) REVERT: D 59 LEU cc_start: 0.9400 (tp) cc_final: 0.9183 (tt) REVERT: D 79 ARG cc_start: 0.7929 (tmt170) cc_final: 0.7682 (tpt170) REVERT: D 110 ARG cc_start: 0.9051 (mtt-85) cc_final: 0.8762 (mtm-85) REVERT: D 124 THR cc_start: 0.9076 (m) cc_final: 0.8415 (m) REVERT: D 137 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8148 (tttm) REVERT: D 143 ILE cc_start: 0.9287 (pp) cc_final: 0.9055 (mm) REVERT: D 154 ASP cc_start: 0.7857 (t0) cc_final: 0.7572 (t0) REVERT: D 155 CYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7242 (m) REVERT: D 165 TYR cc_start: 0.8487 (m-10) cc_final: 0.8235 (m-10) REVERT: E 9 ILE cc_start: 0.9324 (mt) cc_final: 0.9045 (tt) REVERT: E 25 GLN cc_start: 0.9207 (mt0) cc_final: 0.8827 (mt0) REVERT: E 38 MET cc_start: 0.8751 (mmt) cc_final: 0.8242 (tmm) REVERT: E 62 LYS cc_start: 0.9648 (tptt) cc_final: 0.9393 (tppt) REVERT: E 72 SER cc_start: 0.8976 (m) cc_final: 0.8667 (t) REVERT: E 73 GLN cc_start: 0.9237 (pm20) cc_final: 0.8976 (pm20) REVERT: E 74 TYR cc_start: 0.8855 (m-80) cc_final: 0.8384 (m-10) REVERT: E 81 LYS cc_start: 0.8793 (tttp) cc_final: 0.8593 (mttm) REVERT: E 109 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8855 (tt0) REVERT: E 115 LEU cc_start: 0.9418 (tp) cc_final: 0.9161 (tt) REVERT: E 122 PHE cc_start: 0.9615 (m-80) cc_final: 0.9218 (m-10) REVERT: E 123 ASP cc_start: 0.9348 (m-30) cc_final: 0.9088 (t70) REVERT: E 167 ASP cc_start: 0.9256 (t0) cc_final: 0.8809 (t0) REVERT: E 173 LEU cc_start: 0.9618 (mm) cc_final: 0.9312 (tp) REVERT: F 21 ASN cc_start: 0.8500 (m-40) cc_final: 0.7992 (t0) REVERT: F 25 ASP cc_start: 0.9214 (m-30) cc_final: 0.8588 (m-30) REVERT: F 27 LEU cc_start: 0.9327 (mt) cc_final: 0.8751 (pp) REVERT: F 29 ASN cc_start: 0.9315 (m-40) cc_final: 0.8960 (m110) REVERT: F 33 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8968 (mp0) REVERT: F 35 ASN cc_start: 0.9283 (m-40) cc_final: 0.8973 (m-40) REVERT: F 62 GLU cc_start: 0.9614 (tt0) cc_final: 0.9356 (tm-30) REVERT: F 65 GLN cc_start: 0.9341 (pm20) cc_final: 0.8970 (mm-40) REVERT: F 76 TYR cc_start: 0.8862 (t80) cc_final: 0.8543 (t80) REVERT: F 93 ARG cc_start: 0.9332 (ttp80) cc_final: 0.8818 (ttp-110) REVERT: F 103 ASP cc_start: 0.9022 (t0) cc_final: 0.8601 (t0) REVERT: F 115 LEU cc_start: 0.9145 (tp) cc_final: 0.8719 (tp) REVERT: F 117 GLU cc_start: 0.9525 (pp20) cc_final: 0.9004 (pp20) REVERT: F 118 THR cc_start: 0.9623 (m) cc_final: 0.9237 (p) REVERT: F 131 VAL cc_start: 0.8606 (t) cc_final: 0.8312 (t) REVERT: F 136 MET cc_start: 0.8922 (mtm) cc_final: 0.8637 (ttp) REVERT: F 138 ASP cc_start: 0.9007 (m-30) cc_final: 0.8698 (t70) REVERT: F 146 ASP cc_start: 0.9001 (t0) cc_final: 0.8791 (t0) REVERT: F 158 LEU cc_start: 0.8763 (tp) cc_final: 0.8254 (tt) REVERT: F 159 MET cc_start: 0.9075 (mmp) cc_final: 0.8751 (mmt) REVERT: F 165 TYR cc_start: 0.9296 (m-80) cc_final: 0.8940 (m-10) REVERT: G 18 PHE cc_start: 0.8366 (m-80) cc_final: 0.6659 (m-80) REVERT: G 42 ARG cc_start: 0.7986 (mtt-85) cc_final: 0.7706 (ttt90) REVERT: G 53 ASP cc_start: 0.9266 (m-30) cc_final: 0.9002 (p0) REVERT: G 62 LYS cc_start: 0.9424 (tptm) cc_final: 0.9133 (tppt) REVERT: G 74 TYR cc_start: 0.8954 (m-80) cc_final: 0.8637 (m-10) REVERT: G 79 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8898 (pp20) REVERT: G 94 MET cc_start: 0.9177 (mmm) cc_final: 0.8924 (mtt) REVERT: G 97 TYR cc_start: 0.9529 (m-10) cc_final: 0.9126 (m-10) REVERT: G 122 PHE cc_start: 0.9312 (m-80) cc_final: 0.8896 (m-10) REVERT: G 124 LEU cc_start: 0.9124 (mt) cc_final: 0.8892 (mt) REVERT: G 129 TYR cc_start: 0.9132 (m-80) cc_final: 0.8467 (m-80) REVERT: G 161 GLU cc_start: 0.9533 (mt-10) cc_final: 0.9300 (mt-10) REVERT: G 166 ILE cc_start: 0.9341 (mt) cc_final: 0.9121 (tt) REVERT: G 167 ASP cc_start: 0.9273 (t0) cc_final: 0.8792 (t0) REVERT: G 170 ILE cc_start: 0.9536 (mt) cc_final: 0.9221 (pt) REVERT: H 3 ASP cc_start: 0.9618 (p0) cc_final: 0.9072 (m-30) REVERT: H 15 ARG cc_start: 0.8360 (mmm160) cc_final: 0.7911 (mmt-90) REVERT: H 24 PHE cc_start: 0.8708 (m-80) cc_final: 0.8332 (m-10) REVERT: H 42 ASN cc_start: 0.9105 (t0) cc_final: 0.8882 (t0) REVERT: H 60 PHE cc_start: 0.8763 (m-80) cc_final: 0.8360 (m-10) REVERT: H 63 GLN cc_start: 0.9338 (mt0) cc_final: 0.8848 (mt0) REVERT: H 87 ASP cc_start: 0.9278 (m-30) cc_final: 0.8588 (m-30) REVERT: H 97 TYR cc_start: 0.9368 (m-10) cc_final: 0.8779 (m-10) REVERT: H 103 ASP cc_start: 0.9194 (t0) cc_final: 0.8992 (t0) REVERT: H 107 LEU cc_start: 0.9666 (tp) cc_final: 0.9448 (tt) REVERT: H 117 GLU cc_start: 0.9054 (tp30) cc_final: 0.8332 (tp30) REVERT: H 141 ILE cc_start: 0.9359 (tp) cc_final: 0.8839 (tp) REVERT: H 146 ASP cc_start: 0.8432 (t0) cc_final: 0.8183 (t0) REVERT: H 159 MET cc_start: 0.9024 (mmt) cc_final: 0.8542 (mmt) REVERT: I 51 LEU cc_start: 0.9420 (mt) cc_final: 0.9202 (mt) REVERT: I 60 TYR cc_start: 0.8359 (m-10) cc_final: 0.7923 (m-80) REVERT: I 62 LYS cc_start: 0.9367 (tptm) cc_final: 0.8893 (tptt) REVERT: I 91 TYR cc_start: 0.8929 (m-80) cc_final: 0.8720 (m-80) REVERT: I 107 MET cc_start: 0.9275 (tpp) cc_final: 0.9004 (tpt) REVERT: I 110 TYR cc_start: 0.9249 (m-10) cc_final: 0.8737 (m-10) REVERT: I 111 LEU cc_start: 0.9400 (tp) cc_final: 0.8874 (tp) REVERT: I 115 LEU cc_start: 0.9144 (tp) cc_final: 0.8936 (tp) REVERT: I 118 ILE cc_start: 0.9432 (mm) cc_final: 0.9225 (mm) REVERT: I 167 ASP cc_start: 0.9685 (m-30) cc_final: 0.9441 (m-30) REVERT: J 15 ARG cc_start: 0.8579 (mtm180) cc_final: 0.8305 (mtp-110) REVERT: J 17 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8148 (mp0) REVERT: J 35 ASN cc_start: 0.9114 (m110) cc_final: 0.8404 (t0) REVERT: J 38 LEU cc_start: 0.9411 (mt) cc_final: 0.9034 (mp) REVERT: J 60 PHE cc_start: 0.9212 (m-80) cc_final: 0.8959 (m-80) REVERT: J 97 TYR cc_start: 0.8736 (m-10) cc_final: 0.8270 (m-10) REVERT: J 141 ILE cc_start: 0.8572 (tt) cc_final: 0.7785 (tp) REVERT: K 18 PHE cc_start: 0.8859 (m-80) cc_final: 0.8538 (m-80) REVERT: K 19 LEU cc_start: 0.9293 (mt) cc_final: 0.8902 (tt) REVERT: K 21 ASN cc_start: 0.8925 (p0) cc_final: 0.8663 (t0) REVERT: K 33 ARG cc_start: 0.8774 (mtp85) cc_final: 0.8292 (tpm170) REVERT: K 38 MET cc_start: 0.8981 (mmt) cc_final: 0.8737 (mmp) REVERT: K 61 GLN cc_start: 0.9090 (mt0) cc_final: 0.8663 (mt0) REVERT: K 98 CYS cc_start: 0.8733 (t) cc_final: 0.8438 (t) REVERT: K 107 MET cc_start: 0.9095 (tpp) cc_final: 0.8754 (tpp) REVERT: K 115 LEU cc_start: 0.9005 (tp) cc_final: 0.8524 (tp) REVERT: K 122 PHE cc_start: 0.8509 (m-10) cc_final: 0.8253 (m-10) REVERT: K 125 SER cc_start: 0.9260 (t) cc_final: 0.8920 (p) REVERT: K 133 LEU cc_start: 0.9435 (mt) cc_final: 0.9168 (mt) REVERT: K 140 HIS cc_start: 0.8938 (p-80) cc_final: 0.8617 (p-80) REVERT: K 163 ASN cc_start: 0.9456 (m-40) cc_final: 0.8961 (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: 0.8718 (m-10) REVERT: L 65 GLN cc_start: 0.9305 (pt0) cc_final: 0.8935 (pm20) REVERT: L 68 GLN cc_start: 0.9452 (mt0) cc_final: 0.9225 (pp30) REVERT: L 80 ARG cc_start: 0.9079 (mtm-85) cc_final: 0.8850 (mtt180) REVERT: L 89 GLU cc_start: 0.9053 (pp20) cc_final: 0.8642 (pp20) REVERT: L 90 ILE cc_start: 0.9373 (mt) cc_final: 0.8792 (mm) REVERT: L 93 ARG cc_start: 0.8926 (ttp80) cc_final: 0.8543 (ttp-170) REVERT: L 113 ASN cc_start: 0.9189 (t0) cc_final: 0.8432 (t0) REVERT: L 137 LYS cc_start: 0.9607 (tttt) cc_final: 0.9249 (ttmt) REVERT: L 159 MET cc_start: 0.8953 (mmp) cc_final: 0.8709 (mmt) REVERT: L 165 TYR cc_start: 0.9097 (m-80) cc_final: 0.8874 (m-80) REVERT: M 1 MET cc_start: 0.8127 (mpp) cc_final: 0.7656 (ptp) REVERT: M 2 LYS cc_start: 0.8665 (tttp) cc_final: 0.8450 (ttmm) REVERT: M 33 ARG cc_start: 0.9240 (mmt180) cc_final: 0.8503 (tpp-160) REVERT: M 57 GLN cc_start: 0.9602 (mm-40) cc_final: 0.9380 (mm-40) REVERT: M 69 MET cc_start: 0.9518 (tpt) cc_final: 0.9159 (tpt) REVERT: M 81 LYS cc_start: 0.8988 (tmtt) cc_final: 0.8737 (mtpp) REVERT: M 91 TYR cc_start: 0.9271 (m-80) cc_final: 0.8922 (m-10) REVERT: M 129 TYR cc_start: 0.8963 (m-80) cc_final: 0.8657 (m-80) REVERT: M 135 TYR cc_start: 0.8994 (t80) cc_final: 0.8730 (t80) REVERT: M 161 GLU cc_start: 0.9461 (tt0) cc_final: 0.9153 (mt-10) REVERT: N 3 ASP cc_start: 0.8751 (p0) cc_final: 0.8537 (p0) REVERT: N 19 LEU cc_start: 0.8470 (mt) cc_final: 0.8234 (mm) REVERT: N 35 ASN cc_start: 0.9352 (m-40) cc_final: 0.9126 (t0) REVERT: N 36 LYS cc_start: 0.8569 (mttt) cc_final: 0.8312 (mmtt) REVERT: N 62 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8368 (tm-30) REVERT: N 67 ILE cc_start: 0.9720 (pt) cc_final: 0.9251 (mt) REVERT: N 80 ARG cc_start: 0.9408 (mtm-85) cc_final: 0.8452 (mtm-85) REVERT: N 88 MET cc_start: 0.9055 (ttp) cc_final: 0.8757 (ttp) REVERT: N 95 VAL cc_start: 0.9780 (t) cc_final: 0.9543 (p) REVERT: N 103 ASP cc_start: 0.8495 (t0) cc_final: 0.8180 (t0) REVERT: N 115 LEU cc_start: 0.9594 (tp) cc_final: 0.9323 (tp) REVERT: N 148 ASN cc_start: 0.9041 (m-40) cc_final: 0.8839 (p0) REVERT: N 165 TYR cc_start: 0.8824 (m-80) cc_final: 0.8353 (m-10) REVERT: N 167 ASP cc_start: 0.9300 (m-30) cc_final: 0.9046 (m-30) REVERT: O 13 ASP cc_start: 0.9286 (t70) cc_final: 0.9070 (t70) REVERT: O 25 GLN cc_start: 0.8456 (mt0) cc_final: 0.8254 (mt0) REVERT: O 32 LYS cc_start: 0.9210 (mmmt) cc_final: 0.8868 (mmmm) REVERT: O 47 ASN cc_start: 0.9300 (m-40) cc_final: 0.9093 (p0) REVERT: O 99 LEU cc_start: 0.9182 (mt) cc_final: 0.8886 (tp) REVERT: O 104 THR cc_start: 0.9207 (p) cc_final: 0.8866 (p) REVERT: O 118 ILE cc_start: 0.8858 (mt) cc_final: 0.8658 (mt) REVERT: O 129 TYR cc_start: 0.8843 (m-80) cc_final: 0.8226 (m-80) REVERT: O 131 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8842 (tm-30) REVERT: O 166 ILE cc_start: 0.9120 (mt) cc_final: 0.8870 (tt) REVERT: P 1 MET cc_start: 0.6960 (ptt) cc_final: 0.6580 (ptt) REVERT: P 9 VAL cc_start: 0.9724 (t) cc_final: 0.9498 (p) REVERT: P 11 GLN cc_start: 0.8735 (mt0) cc_final: 0.8418 (mt0) REVERT: P 23 GLN cc_start: 0.8425 (mt0) cc_final: 0.8157 (mt0) REVERT: P 67 ILE cc_start: 0.9154 (pt) cc_final: 0.8793 (tp) REVERT: P 93 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8426 (ttp-170) REVERT: P 94 TYR cc_start: 0.9219 (m-80) cc_final: 0.8404 (m-80) REVERT: P 97 TYR cc_start: 0.9182 (m-10) cc_final: 0.8578 (m-80) REVERT: P 104 SER cc_start: 0.9362 (p) cc_final: 0.9105 (p) REVERT: P 110 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7780 (mtp85) REVERT: P 156 SER cc_start: 0.8692 (t) cc_final: 0.8358 (m) REVERT: P 159 MET cc_start: 0.9175 (mmm) cc_final: 0.8269 (tmm) REVERT: P 162 ILE cc_start: 0.9528 (pt) cc_final: 0.9278 (pt) REVERT: Q 14 THR cc_start: 0.8687 (p) cc_final: 0.8188 (t) REVERT: Q 15 GLN cc_start: 0.8509 (mm110) cc_final: 0.8222 (mm110) REVERT: Q 24 LEU cc_start: 0.8432 (mt) cc_final: 0.7748 (mt) REVERT: Q 37 SER cc_start: 0.7989 (m) cc_final: 0.7148 (p) REVERT: Q 53 ASP cc_start: 0.7168 (m-30) cc_final: 0.6729 (m-30) REVERT: Q 57 GLN cc_start: 0.6950 (mm110) cc_final: 0.6678 (mm-40) REVERT: Q 73 GLN cc_start: 0.7797 (pm20) cc_final: 0.7084 (pm20) REVERT: Q 86 ARG cc_start: 0.5640 (OUTLIER) cc_final: 0.4764 (mmt90) REVERT: Q 107 MET cc_start: 0.8564 (ttm) cc_final: 0.8000 (mtp) REVERT: Q 108 ASP cc_start: 0.8587 (m-30) cc_final: 0.8205 (m-30) REVERT: R 38 LEU cc_start: 0.8563 (mt) cc_final: 0.8268 (mp) REVERT: R 39 ASP cc_start: 0.7872 (m-30) cc_final: 0.7661 (m-30) REVERT: R 87 ASP cc_start: 0.7926 (m-30) cc_final: 0.7655 (m-30) REVERT: R 88 MET cc_start: 0.9649 (mmm) cc_final: 0.9054 (mtp) REVERT: R 103 ASP cc_start: 0.7354 (t0) cc_final: 0.6883 (t0) REVERT: R 111 CYS cc_start: 0.8829 (t) cc_final: 0.8615 (t) REVERT: R 115 LEU cc_start: 0.9287 (tt) cc_final: 0.8835 (tt) REVERT: R 159 MET cc_start: 0.8829 (mmp) cc_final: 0.8077 (ptt) REVERT: S 37 SER cc_start: 0.8987 (t) cc_final: 0.8766 (p) REVERT: S 44 LEU cc_start: 0.9496 (mt) cc_final: 0.8674 (tp) REVERT: S 57 GLN cc_start: 0.9277 (mm-40) cc_final: 0.9065 (mm-40) REVERT: S 73 GLN cc_start: 0.9059 (pt0) cc_final: 0.8828 (pm20) REVERT: S 74 TYR cc_start: 0.9331 (m-80) cc_final: 0.8955 (m-80) REVERT: S 79 GLU cc_start: 0.8643 (mp0) cc_final: 0.8403 (tm-30) REVERT: S 83 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8262 (mmtm) REVERT: S 90 TYR cc_start: 0.8802 (m-10) cc_final: 0.8297 (m-10) REVERT: S 115 LEU cc_start: 0.9076 (tp) cc_final: 0.8870 (tp) REVERT: S 118 ILE cc_start: 0.9581 (OUTLIER) cc_final: 0.9365 (pp) REVERT: T 9 VAL cc_start: 0.9299 (t) cc_final: 0.9057 (p) REVERT: T 13 ASP cc_start: 0.8990 (t70) cc_final: 0.8666 (t0) REVERT: T 15 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7121 (mmt-90) REVERT: T 18 PHE cc_start: 0.8218 (m-80) cc_final: 0.7952 (m-80) REVERT: T 19 LEU cc_start: 0.8129 (mt) cc_final: 0.7754 (mm) REVERT: T 23 GLN cc_start: 0.8537 (mt0) cc_final: 0.8263 (mp10) REVERT: T 35 ASN cc_start: 0.8016 (m-40) cc_final: 0.7760 (p0) REVERT: T 76 TYR cc_start: 0.4893 (t80) cc_final: 0.4634 (t80) REVERT: T 87 ASP cc_start: 0.8707 (m-30) cc_final: 0.8491 (m-30) REVERT: U 18 PHE cc_start: 0.8657 (m-80) cc_final: 0.8426 (m-80) REVERT: U 25 GLN cc_start: 0.9058 (mt0) cc_final: 0.8706 (tt0) REVERT: U 61 GLN cc_start: 0.8053 (mt0) cc_final: 0.7604 (pp30) REVERT: U 62 LYS cc_start: 0.9275 (tppp) cc_final: 0.9046 (tptt) REVERT: U 69 MET cc_start: 0.7094 (mtt) cc_final: 0.6507 (tpp) REVERT: U 87 ASP cc_start: 0.7572 (m-30) cc_final: 0.7274 (m-30) REVERT: U 94 MET cc_start: 0.9494 (tpp) cc_final: 0.9208 (tpp) REVERT: U 117 GLU cc_start: 0.9116 (tt0) cc_final: 0.8854 (mp0) REVERT: U 123 ASP cc_start: 0.8995 (t0) cc_final: 0.8723 (t70) REVERT: U 140 HIS cc_start: 0.9408 (p-80) cc_final: 0.9192 (p-80) REVERT: U 173 LEU cc_start: 0.9399 (mt) cc_final: 0.8934 (mt) REVERT: V 5 PHE cc_start: 0.8626 (m-10) cc_final: 0.8300 (m-10) REVERT: V 11 GLN cc_start: 0.8841 (tt0) cc_final: 0.8459 (tp40) REVERT: V 13 ASP cc_start: 0.9198 (t70) cc_final: 0.8699 (t0) REVERT: V 15 ARG cc_start: 0.9393 (mtm110) cc_final: 0.9060 (mtm-85) REVERT: V 17 GLU cc_start: 0.8531 (mp0) cc_final: 0.8274 (mp0) REVERT: V 60 PHE cc_start: 0.8876 (m-80) cc_final: 0.8622 (m-80) REVERT: V 62 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8854 (tm-30) REVERT: V 81 MET cc_start: 0.8779 (tpp) cc_final: 0.8537 (tpp) REVERT: V 93 ARG cc_start: 0.9402 (ttp80) cc_final: 0.8923 (ttp80) REVERT: V 97 TYR cc_start: 0.9288 (m-10) cc_final: 0.8861 (m-80) REVERT: V 108 ASP cc_start: 0.9303 (m-30) cc_final: 0.9068 (t0) REVERT: V 159 MET cc_start: 0.9029 (mmp) cc_final: 0.8617 (tmm) REVERT: V 168 ARG cc_start: 0.9110 (ttt90) cc_final: 0.8898 (mmm-85) REVERT: W 22 THR cc_start: 0.9502 (p) cc_final: 0.9290 (p) REVERT: W 33 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7883 (tmm160) REVERT: W 42 ARG cc_start: 0.6776 (tpp80) cc_final: 0.6286 (tpp80) REVERT: W 46 ASN cc_start: 0.7349 (m-40) cc_final: 0.6971 (p0) REVERT: W 65 TYR cc_start: 0.8423 (p90) cc_final: 0.7729 (p90) REVERT: W 69 MET cc_start: 0.4555 (mtp) cc_final: 0.4112 (mmm) REVERT: W 96 THR cc_start: 0.7919 (p) cc_final: 0.7677 (t) REVERT: W 97 TYR cc_start: 0.8508 (m-10) cc_final: 0.7985 (m-80) REVERT: W 107 MET cc_start: 0.8741 (mmp) cc_final: 0.8484 (mmm) REVERT: W 111 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7686 (pt) REVERT: X 5 PHE cc_start: 0.8067 (m-80) cc_final: 0.7498 (m-80) REVERT: X 38 LEU cc_start: 0.9434 (mt) cc_final: 0.9180 (mt) REVERT: X 79 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7321 (tpm170) REVERT: X 89 GLU cc_start: 0.8940 (tt0) cc_final: 0.8639 (tm-30) REVERT: X 119 TYR cc_start: 0.8045 (m-80) cc_final: 0.7833 (m-80) REVERT: X 136 MET cc_start: 0.7261 (mtm) cc_final: 0.6612 (mtp) REVERT: X 166 PHE cc_start: 0.8073 (m-80) cc_final: 0.7574 (m-80) REVERT: Y 20 PHE cc_start: 0.8967 (m-80) cc_final: 0.8137 (m-10) REVERT: Y 36 MET cc_start: 0.7413 (ttp) cc_final: 0.6911 (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: 0.9257 (p) REVERT: Y 55 MET cc_start: 0.9156 (ttp) cc_final: 0.8735 (ttp) REVERT: Z 9 ARG cc_start: 0.7964 (mmt180) cc_final: 0.7699 (mmm160) REVERT: Z 42 GLN cc_start: 0.9071 (tp40) cc_final: 0.8792 (tp40) REVERT: Z 44 LEU cc_start: 0.9176 (mt) cc_final: 0.8939 (mt) REVERT: Z 59 GLU cc_start: 0.8954 (mp0) cc_final: 0.8367 (pt0) REVERT: Z 64 ASN cc_start: 0.9151 (t0) cc_final: 0.8861 (t0) REVERT: Z 78 LYS cc_start: 0.9246 (mttt) cc_final: 0.8672 (ttpt) REVERT: Z 91 PHE cc_start: 0.9165 (t80) cc_final: 0.8099 (t80) REVERT: Z 93 THR cc_start: 0.9479 (m) cc_final: 0.9260 (m) REVERT: Z 101 LYS cc_start: 0.9308 (tttt) cc_final: 0.9029 (ttpp) REVERT: Z 109 TYR cc_start: 0.7807 (m-10) cc_final: 0.7480 (m-10) REVERT: Z 119 ASP cc_start: 0.9445 (m-30) cc_final: 0.8946 (m-30) REVERT: Z 127 ASP cc_start: 0.8993 (m-30) cc_final: 0.8462 (t0) REVERT: Z 150 TYR cc_start: 0.8672 (p90) cc_final: 0.8456 (p90) REVERT: Z 160 GLN cc_start: 0.7988 (pt0) cc_final: 0.7690 (pt0) REVERT: Z 179 ASP cc_start: 0.9431 (m-30) cc_final: 0.8981 (m-30) REVERT: Z 182 GLN cc_start: 0.8526 (tt0) cc_final: 0.8307 (tt0) REVERT: Z 184 GLU cc_start: 0.9131 (pt0) cc_final: 0.8816 (mp0) REVERT: Z 187 MET cc_start: 0.9344 (tmt) cc_final: 0.9013 (mtp) REVERT: Z 196 THR cc_start: 0.9607 (p) cc_final: 0.9357 (t) REVERT: Z 264 TYR cc_start: 0.9255 (t80) cc_final: 0.8861 (t80) REVERT: Z 270 LYS cc_start: 0.9423 (tppt) cc_final: 0.9060 (tptt) REVERT: Z 275 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8434 (mm-40) REVERT: a 3 ILE cc_start: 0.7564 (mm) cc_final: 0.6827 (mm) REVERT: a 21 GLU cc_start: 0.8911 (pt0) cc_final: 0.7832 (tp30) REVERT: a 38 ASP cc_start: 0.7895 (p0) cc_final: 0.7496 (p0) REVERT: a 74 ASN cc_start: 0.9413 (t0) cc_final: 0.8990 (p0) REVERT: a 82 PHE cc_start: 0.9062 (t80) cc_final: 0.8768 (t80) REVERT: a 88 LYS cc_start: 0.9607 (pttt) cc_final: 0.9206 (tptp) REVERT: a 124 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7942 (tt0) REVERT: a 152 ASN cc_start: 0.9214 (m-40) cc_final: 0.9003 (t0) REVERT: a 165 TYR cc_start: 0.5759 (t80) cc_final: 0.5345 (m-10) REVERT: a 170 PHE cc_start: 0.8396 (m-10) cc_final: 0.7933 (m-80) outliers start: 25 outliers final: 8 residues processed: 2180 average time/residue: 0.5096 time to fit residues: 1744.6026 Evaluate side-chains 1583 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1569 time to evaluate : 3.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 378 optimal weight: 10.0000 chunk 339 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 chunk 351 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 406 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 171 ASN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN D 35 ASN E 15 GLN E 21 ASN E 61 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 GLN G 171 ASN H 35 ASN H 145 ASN I 15 GLN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN M 140 HIS O 139 ASN P 47 ASN R 63 GLN R 134 GLN R 148 ASN S 15 GLN T 21 ASN U 15 GLN U 119 ASN U 163 ASN ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 21 ASN X 42 ASN ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 92 GLN Z 266 GLN Z 272 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: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 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 0.069 36155 Z= 0.267 Angle : 0.762 43.059 49243 Z= 0.352 Chirality : 0.039 0.220 5448 Planarity : 0.005 0.128 6402 Dihedral : 10.903 89.982 6599 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.18 % Favored : 97.77 % Rotamer: Outliers : 0.24 % Allowed : 3.86 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.12), residues: 4448 helix: 1.32 (0.08), residues: 3355 sheet: 1.85 (1.01), residues: 28 loop : -0.93 (0.21), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP U 128 HIS 0.005 0.001 HIS U 140 PHE 0.029 0.002 PHE V 166 TYR 0.041 0.002 TYR M 97 ARG 0.008 0.001 ARG U 33 *********************** 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 1796 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1788 time to evaluate : 3.753 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: 0.7954 (ttpt) cc_final: 0.7332 (ttpt) REVERT: A 18 PHE cc_start: 0.8177 (m-80) cc_final: 0.7572 (m-80) REVERT: A 30 ARG cc_start: 0.8899 (tpt-90) cc_final: 0.8634 (tmt170) REVERT: A 33 ARG cc_start: 0.9119 (mmm160) cc_final: 0.8636 (tpt170) REVERT: A 38 MET cc_start: 0.9257 (mmt) cc_final: 0.8230 (tmm) REVERT: A 39 GLU cc_start: 0.9620 (tp30) cc_final: 0.9148 (mt-10) REVERT: A 62 LYS cc_start: 0.9063 (tptt) cc_final: 0.8675 (tptt) REVERT: A 63 PHE cc_start: 0.9224 (m-80) cc_final: 0.8867 (m-80) REVERT: A 90 TYR cc_start: 0.9227 (m-10) cc_final: 0.8983 (m-10) REVERT: A 94 MET cc_start: 0.9753 (tpp) cc_final: 0.9293 (tpp) REVERT: A 109 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8533 (mt-10) REVERT: A 129 TYR cc_start: 0.9000 (m-80) cc_final: 0.8798 (m-80) REVERT: A 167 ASP cc_start: 0.9185 (t0) cc_final: 0.8802 (t0) REVERT: B 32 LYS cc_start: 0.8981 (ttpp) cc_final: 0.8700 (tppt) REVERT: B 78 ASN cc_start: 0.8478 (t0) cc_final: 0.8264 (t0) REVERT: B 88 MET cc_start: 0.9382 (mtm) cc_final: 0.9173 (tpp) REVERT: B 89 GLU cc_start: 0.9372 (pt0) cc_final: 0.8880 (tt0) REVERT: B 119 TYR cc_start: 0.9486 (m-80) cc_final: 0.8436 (m-80) REVERT: B 120 GLN cc_start: 0.8759 (mt0) cc_final: 0.8098 (tm-30) REVERT: B 136 MET cc_start: 0.8965 (mtt) cc_final: 0.6912 (mtt) REVERT: B 145 ASN cc_start: 0.9077 (t0) cc_final: 0.8491 (p0) REVERT: B 159 MET cc_start: 0.9542 (mpp) cc_final: 0.9222 (mpp) REVERT: C 65 TYR cc_start: 0.7613 (p90) cc_final: 0.7375 (p90) REVERT: C 69 MET cc_start: 0.7590 (ttm) cc_final: 0.7035 (ttm) REVERT: C 94 MET cc_start: 0.9477 (mmt) cc_final: 0.9054 (mmm) REVERT: D 32 LYS cc_start: 0.9442 (ptmt) cc_final: 0.9215 (pttt) REVERT: D 97 TYR cc_start: 0.9290 (m-10) cc_final: 0.8612 (m-80) REVERT: D 128 SER cc_start: 0.9314 (p) cc_final: 0.9067 (p) REVERT: D 154 ASP cc_start: 0.7840 (t0) cc_final: 0.7565 (t0) REVERT: D 159 MET cc_start: 0.9485 (mmp) cc_final: 0.8831 (mpp) REVERT: E 15 GLN cc_start: 0.8747 (mt0) cc_final: 0.8280 (mt0) REVERT: E 17 ARG cc_start: 0.8965 (ptp-110) cc_final: 0.8636 (ttp-110) REVERT: E 25 GLN cc_start: 0.9109 (mt0) cc_final: 0.8737 (mt0) REVERT: E 38 MET cc_start: 0.8843 (mmt) cc_final: 0.8178 (tmm) REVERT: E 53 ASP cc_start: 0.9593 (m-30) cc_final: 0.9384 (p0) REVERT: E 57 GLN cc_start: 0.8708 (mm110) cc_final: 0.8508 (mm-40) REVERT: E 62 LYS cc_start: 0.9539 (tptt) cc_final: 0.9156 (tppt) REVERT: E 69 MET cc_start: 0.8892 (mtp) cc_final: 0.8021 (ttm) REVERT: E 72 SER cc_start: 0.8716 (m) cc_final: 0.8489 (t) REVERT: E 73 GLN cc_start: 0.9319 (pm20) cc_final: 0.9049 (pm20) REVERT: E 74 TYR cc_start: 0.8820 (m-80) cc_final: 0.8300 (m-10) REVERT: E 115 LEU cc_start: 0.9143 (tp) cc_final: 0.8886 (tt) REVERT: E 121 THR cc_start: 0.9601 (p) cc_final: 0.9297 (t) REVERT: E 123 ASP cc_start: 0.9088 (m-30) cc_final: 0.8705 (t70) REVERT: E 130 ILE cc_start: 0.9199 (mt) cc_final: 0.8991 (mt) REVERT: E 167 ASP cc_start: 0.9264 (t0) cc_final: 0.8641 (t0) REVERT: F 21 ASN cc_start: 0.8517 (m-40) cc_final: 0.7563 (t0) REVERT: F 23 GLN cc_start: 0.8194 (mt0) cc_final: 0.7958 (mt0) REVERT: F 25 ASP cc_start: 0.8850 (m-30) cc_final: 0.8303 (m-30) REVERT: F 29 ASN cc_start: 0.9550 (m-40) cc_final: 0.9023 (m110) REVERT: F 30 LEU cc_start: 0.9283 (mm) cc_final: 0.9026 (tp) REVERT: F 35 ASN cc_start: 0.9302 (m-40) cc_final: 0.8985 (m-40) REVERT: F 62 GLU cc_start: 0.9559 (tt0) cc_final: 0.9302 (tm-30) REVERT: F 76 TYR cc_start: 0.9134 (t80) cc_final: 0.8205 (t80) REVERT: F 81 MET cc_start: 0.9133 (tpp) cc_final: 0.8900 (tpp) REVERT: F 88 MET cc_start: 0.9222 (tpp) cc_final: 0.8741 (tpp) REVERT: F 103 ASP cc_start: 0.8908 (t0) cc_final: 0.8677 (t70) REVERT: F 118 THR cc_start: 0.9629 (m) cc_final: 0.9378 (p) REVERT: F 136 MET cc_start: 0.8414 (mtm) cc_final: 0.8020 (mtm) REVERT: F 138 ASP cc_start: 0.8990 (m-30) cc_final: 0.8632 (t70) REVERT: F 146 ASP cc_start: 0.8616 (t0) cc_final: 0.8291 (t0) REVERT: F 161 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9121 (tp30) REVERT: F 165 TYR cc_start: 0.9566 (m-80) cc_final: 0.9284 (m-10) REVERT: G 18 PHE cc_start: 0.8407 (m-80) cc_final: 0.8120 (m-80) REVERT: G 28 ASP cc_start: 0.9055 (t0) cc_final: 0.8736 (t70) REVERT: G 62 LYS cc_start: 0.9405 (tptm) cc_final: 0.9122 (tppt) REVERT: G 70 GLN cc_start: 0.8303 (tm-30) cc_final: 0.8012 (pp30) REVERT: G 74 TYR cc_start: 0.9107 (m-80) cc_final: 0.8674 (m-10) REVERT: G 79 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8908 (pp20) REVERT: G 97 TYR cc_start: 0.9445 (m-10) cc_final: 0.9012 (m-10) REVERT: G 98 CYS cc_start: 0.9179 (m) cc_final: 0.8891 (p) REVERT: G 99 LEU cc_start: 0.9277 (tp) cc_final: 0.8810 (tp) REVERT: G 116 SER cc_start: 0.9610 (p) cc_final: 0.9317 (m) REVERT: G 117 GLU cc_start: 0.8873 (tp30) cc_final: 0.8554 (tp30) REVERT: G 119 ASN cc_start: 0.9214 (m110) cc_final: 0.8687 (t0) REVERT: G 122 PHE cc_start: 0.9207 (m-80) cc_final: 0.8812 (m-10) REVERT: G 123 ASP cc_start: 0.8685 (t0) cc_final: 0.8445 (t70) REVERT: G 124 LEU cc_start: 0.9157 (mt) cc_final: 0.8780 (mt) REVERT: G 129 TYR cc_start: 0.9141 (m-80) cc_final: 0.8325 (m-80) REVERT: G 137 LYS cc_start: 0.9591 (ptmt) cc_final: 0.9367 (ttpp) REVERT: G 161 GLU cc_start: 0.9570 (mt-10) cc_final: 0.9318 (mt-10) REVERT: G 167 ASP cc_start: 0.9222 (t0) cc_final: 0.8950 (t0) REVERT: H 15 ARG cc_start: 0.7886 (mmm160) cc_final: 0.7171 (mtm-85) REVERT: H 17 GLU cc_start: 0.9499 (pm20) cc_final: 0.9173 (pm20) REVERT: H 24 PHE cc_start: 0.8380 (m-80) cc_final: 0.8129 (m-80) REVERT: H 52 VAL cc_start: 0.9103 (m) cc_final: 0.8853 (p) REVERT: H 67 ILE cc_start: 0.9695 (pt) cc_final: 0.9310 (tt) REVERT: H 87 ASP cc_start: 0.9424 (m-30) cc_final: 0.8661 (m-30) REVERT: H 91 ILE cc_start: 0.9521 (mm) cc_final: 0.9144 (tp) REVERT: H 97 TYR cc_start: 0.9500 (m-10) cc_final: 0.9101 (m-10) REVERT: H 117 GLU cc_start: 0.9131 (tp30) cc_final: 0.8752 (tp30) REVERT: I 13 ASP cc_start: 0.9253 (t0) cc_final: 0.8861 (t0) REVERT: I 47 ASN cc_start: 0.7924 (p0) cc_final: 0.7614 (p0) REVERT: I 51 LEU cc_start: 0.9360 (mt) cc_final: 0.9028 (mt) REVERT: I 60 TYR cc_start: 0.8172 (m-10) cc_final: 0.7874 (m-80) REVERT: I 62 LYS cc_start: 0.9385 (tptm) cc_final: 0.8800 (tptt) REVERT: I 107 MET cc_start: 0.9241 (tpp) cc_final: 0.9038 (tpt) REVERT: I 110 TYR cc_start: 0.9030 (m-10) cc_final: 0.8693 (m-10) REVERT: I 111 LEU cc_start: 0.9411 (tp) cc_final: 0.9186 (tp) REVERT: I 118 ILE cc_start: 0.9512 (mm) cc_final: 0.9279 (pt) REVERT: I 119 ASN cc_start: 0.9447 (m110) cc_final: 0.9110 (m110) REVERT: I 140 HIS cc_start: 0.9359 (p90) cc_final: 0.8980 (p90) REVERT: I 163 ASN cc_start: 0.9608 (m110) cc_final: 0.9047 (m110) REVERT: I 166 ILE cc_start: 0.9804 (tt) cc_final: 0.9371 (tt) REVERT: I 167 ASP cc_start: 0.9583 (m-30) cc_final: 0.9281 (m-30) REVERT: J 17 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8541 (mp0) REVERT: J 33 GLU cc_start: 0.9381 (tt0) cc_final: 0.9164 (tm-30) REVERT: J 35 ASN cc_start: 0.9164 (m110) cc_final: 0.8363 (t0) REVERT: J 50 THR cc_start: 0.9427 (m) cc_final: 0.9199 (t) REVERT: J 76 TYR cc_start: 0.9317 (t80) cc_final: 0.8424 (t80) REVERT: J 91 ILE cc_start: 0.9521 (tp) cc_final: 0.9321 (tp) REVERT: J 97 TYR cc_start: 0.9019 (m-10) cc_final: 0.8433 (m-10) REVERT: K 87 ASP cc_start: 0.9519 (m-30) cc_final: 0.9242 (m-30) REVERT: K 94 MET cc_start: 0.9047 (mmt) cc_final: 0.8708 (mmt) REVERT: K 107 MET cc_start: 0.8881 (tpp) cc_final: 0.8615 (tpp) REVERT: K 140 HIS cc_start: 0.8699 (p-80) cc_final: 0.8401 (p-80) REVERT: K 161 GLU cc_start: 0.9393 (mt-10) cc_final: 0.8871 (tp30) REVERT: L 2 LEU cc_start: 0.9515 (mt) cc_final: 0.8887 (mt) REVERT: L 13 ASP cc_start: 0.8869 (t70) cc_final: 0.8499 (t0) REVERT: L 41 VAL cc_start: 0.9513 (m) cc_final: 0.9278 (p) REVERT: L 59 LEU cc_start: 0.9500 (tp) cc_final: 0.9253 (tp) REVERT: L 78 ASN cc_start: 0.8931 (t0) cc_final: 0.8690 (t0) REVERT: L 80 ARG cc_start: 0.8976 (mtm-85) cc_final: 0.8650 (mtt180) REVERT: L 81 MET cc_start: 0.9017 (tpp) cc_final: 0.8533 (tpp) REVERT: L 89 GLU cc_start: 0.9199 (pp20) cc_final: 0.8651 (tm-30) REVERT: L 90 ILE cc_start: 0.9263 (mt) cc_final: 0.8592 (mm) REVERT: L 113 ASN cc_start: 0.9369 (t0) cc_final: 0.8659 (t0) REVERT: L 137 LYS cc_start: 0.9431 (tttt) cc_final: 0.8960 (ttmt) REVERT: L 159 MET cc_start: 0.8990 (mmp) cc_final: 0.8777 (mmt) REVERT: L 161 GLU cc_start: 0.8852 (tt0) cc_final: 0.8273 (tp30) REVERT: M 9 ILE cc_start: 0.9229 (tp) cc_final: 0.8835 (tp) REVERT: M 81 LYS cc_start: 0.8968 (tmtt) cc_final: 0.8661 (mtpp) REVERT: M 91 TYR cc_start: 0.9149 (m-80) cc_final: 0.8880 (m-80) REVERT: M 98 CYS cc_start: 0.8206 (m) cc_final: 0.7884 (m) REVERT: M 129 TYR cc_start: 0.8957 (m-80) cc_final: 0.8687 (m-80) REVERT: M 135 TYR cc_start: 0.9179 (t80) cc_final: 0.8901 (t80) REVERT: M 171 ASN cc_start: 0.8890 (p0) cc_final: 0.8431 (p0) REVERT: N 35 ASN cc_start: 0.9451 (m-40) cc_final: 0.9064 (t0) REVERT: N 62 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8752 (tm-30) REVERT: N 65 GLN cc_start: 0.8556 (mp10) cc_final: 0.8202 (mp10) REVERT: N 80 ARG cc_start: 0.9090 (mtm-85) cc_final: 0.8582 (mtm-85) REVERT: N 88 MET cc_start: 0.8976 (ttp) cc_final: 0.7656 (tpt) REVERT: N 97 TYR cc_start: 0.9167 (m-10) cc_final: 0.8539 (m-80) REVERT: N 103 ASP cc_start: 0.8041 (t0) cc_final: 0.7700 (t0) REVERT: N 107 LEU cc_start: 0.9443 (tp) cc_final: 0.9188 (tp) REVERT: N 115 LEU cc_start: 0.9470 (tp) cc_final: 0.9179 (tt) REVERT: N 119 TYR cc_start: 0.9381 (m-10) cc_final: 0.9121 (m-10) REVERT: N 136 MET cc_start: 0.8931 (mtm) cc_final: 0.7859 (mtm) REVERT: N 165 TYR cc_start: 0.8804 (m-80) cc_final: 0.8517 (m-10) REVERT: O 1 MET cc_start: 0.6979 (tpp) cc_final: 0.6702 (tpp) REVERT: O 13 ASP cc_start: 0.9319 (t70) cc_final: 0.9083 (t70) REVERT: O 19 LEU cc_start: 0.8437 (mm) cc_final: 0.8189 (mm) REVERT: O 91 TYR cc_start: 0.9368 (m-80) cc_final: 0.8962 (m-80) REVERT: O 98 CYS cc_start: 0.9205 (p) cc_final: 0.8989 (p) REVERT: O 99 LEU cc_start: 0.9318 (mt) cc_final: 0.9024 (tp) REVERT: O 104 THR cc_start: 0.9153 (p) cc_final: 0.8833 (p) REVERT: O 129 TYR cc_start: 0.9033 (m-80) cc_final: 0.8255 (m-80) REVERT: O 131 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8959 (pt0) REVERT: P 1 MET cc_start: 0.6984 (ptt) cc_final: 0.6536 (ptt) REVERT: P 5 PHE cc_start: 0.9189 (m-10) cc_final: 0.8808 (m-10) REVERT: P 9 VAL cc_start: 0.9747 (t) cc_final: 0.9475 (p) REVERT: P 23 GLN cc_start: 0.8230 (mt0) cc_final: 0.7998 (mt0) REVERT: P 81 MET cc_start: 0.8616 (tpp) cc_final: 0.8356 (tpp) REVERT: P 94 TYR cc_start: 0.9160 (m-80) cc_final: 0.8565 (m-80) REVERT: P 97 TYR cc_start: 0.9164 (m-10) cc_final: 0.8287 (m-80) REVERT: P 113 ASN cc_start: 0.8825 (t0) cc_final: 0.8618 (t0) REVERT: P 124 THR cc_start: 0.8902 (m) cc_final: 0.8627 (p) REVERT: P 159 MET cc_start: 0.8975 (mmm) cc_final: 0.8095 (ppp) REVERT: Q 1 MET cc_start: 0.7470 (mtt) cc_final: 0.7103 (mtt) REVERT: Q 37 SER cc_start: 0.8252 (m) cc_final: 0.7542 (p) REVERT: Q 39 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7559 (mt-10) REVERT: Q 62 LYS cc_start: 0.6340 (tptm) cc_final: 0.6080 (ttmt) REVERT: Q 98 CYS cc_start: 0.8618 (m) cc_final: 0.8328 (m) REVERT: Q 107 MET cc_start: 0.8577 (ttm) cc_final: 0.8320 (mtp) REVERT: Q 108 ASP cc_start: 0.8900 (m-30) cc_final: 0.8617 (m-30) REVERT: R 2 LEU cc_start: 0.5768 (mt) cc_final: 0.5424 (mm) REVERT: R 38 LEU cc_start: 0.8771 (mt) cc_final: 0.8372 (mp) REVERT: R 85 LEU cc_start: 0.9602 (mt) cc_final: 0.9303 (tp) REVERT: R 87 ASP cc_start: 0.8052 (m-30) cc_final: 0.7824 (m-30) REVERT: R 88 MET cc_start: 0.9572 (mmm) cc_final: 0.9272 (mtm) REVERT: R 103 ASP cc_start: 0.7210 (t0) cc_final: 0.6956 (t70) REVERT: R 111 CYS cc_start: 0.8600 (t) cc_final: 0.8089 (t) REVERT: R 128 SER cc_start: 0.8532 (m) cc_final: 0.8254 (m) REVERT: R 146 ASP cc_start: 0.7572 (t0) cc_final: 0.7267 (t0) REVERT: R 159 MET cc_start: 0.8670 (mmp) cc_final: 0.8150 (ptt) REVERT: R 162 ILE cc_start: 0.9005 (mt) cc_final: 0.8700 (mt) REVERT: S 28 ASP cc_start: 0.8929 (t0) cc_final: 0.8684 (t0) REVERT: S 37 SER cc_start: 0.9203 (t) cc_final: 0.8799 (p) REVERT: S 44 LEU cc_start: 0.9664 (mt) cc_final: 0.9043 (tp) REVERT: S 49 GLN cc_start: 0.9397 (tp-100) cc_final: 0.8685 (pm20) REVERT: S 73 GLN cc_start: 0.9076 (pt0) cc_final: 0.8859 (pm20) REVERT: S 74 TYR cc_start: 0.9283 (m-80) cc_final: 0.8886 (m-80) REVERT: S 79 GLU cc_start: 0.8542 (mp0) cc_final: 0.8244 (tm-30) REVERT: S 83 LYS cc_start: 0.9021 (mmtp) cc_final: 0.8464 (mmtm) REVERT: S 84 CYS cc_start: 0.9032 (t) cc_final: 0.8777 (t) REVERT: S 90 TYR cc_start: 0.8924 (m-10) cc_final: 0.8516 (m-10) REVERT: S 115 LEU cc_start: 0.8674 (tp) cc_final: 0.8465 (tp) REVERT: S 137 LYS cc_start: 0.9246 (ttpt) cc_final: 0.9026 (tptt) REVERT: T 15 ARG cc_start: 0.8290 (mtp85) cc_final: 0.7435 (mmp80) REVERT: T 18 PHE cc_start: 0.8109 (m-80) cc_final: 0.7894 (m-10) REVERT: T 19 LEU cc_start: 0.8090 (mt) cc_final: 0.7585 (mm) REVERT: T 23 GLN cc_start: 0.8419 (mt0) cc_final: 0.7968 (mp10) REVERT: T 27 LEU cc_start: 0.9136 (mt) cc_final: 0.8865 (mt) REVERT: T 35 ASN cc_start: 0.7694 (m-40) cc_final: 0.7318 (p0) REVERT: T 47 ASN cc_start: 0.8006 (t0) cc_final: 0.7748 (t0) REVERT: T 104 SER cc_start: 0.9365 (p) cc_final: 0.9158 (t) REVERT: T 141 ILE cc_start: 0.8526 (mt) cc_final: 0.8325 (mt) REVERT: T 161 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8320 (mm-30) REVERT: T 162 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8798 (mt) REVERT: T 165 TYR cc_start: 0.8554 (m-80) cc_final: 0.7796 (m-80) REVERT: U 18 PHE cc_start: 0.8774 (m-80) cc_final: 0.8467 (m-10) REVERT: U 24 LEU cc_start: 0.9399 (mt) cc_final: 0.9128 (mt) REVERT: U 28 ASP cc_start: 0.9249 (t0) cc_final: 0.9030 (t0) REVERT: U 69 MET cc_start: 0.7352 (mtt) cc_final: 0.6764 (tpp) REVERT: U 115 LEU cc_start: 0.8749 (tp) cc_final: 0.8444 (tp) REVERT: U 117 GLU cc_start: 0.9057 (tt0) cc_final: 0.8827 (mp0) REVERT: U 123 ASP cc_start: 0.9208 (t0) cc_final: 0.8801 (t0) REVERT: U 140 HIS cc_start: 0.9334 (p-80) cc_final: 0.9100 (p-80) REVERT: U 171 ASN cc_start: 0.8976 (t0) cc_final: 0.8701 (t0) REVERT: V 11 GLN cc_start: 0.8843 (tt0) cc_final: 0.8359 (tp40) REVERT: V 19 LEU cc_start: 0.9396 (mt) cc_final: 0.9096 (mt) REVERT: V 62 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8905 (tm-30) REVERT: V 68 GLN cc_start: 0.8918 (pt0) cc_final: 0.8518 (pt0) REVERT: V 78 ASN cc_start: 0.7960 (t0) cc_final: 0.7602 (t0) REVERT: V 81 MET cc_start: 0.8657 (tpp) cc_final: 0.8048 (tpp) REVERT: V 108 ASP cc_start: 0.9244 (m-30) cc_final: 0.9029 (t0) REVERT: V 113 ASN cc_start: 0.8579 (t0) cc_final: 0.8137 (t0) REVERT: V 137 LYS cc_start: 0.9121 (tttt) cc_final: 0.8395 (tptt) REVERT: V 150 ILE cc_start: 0.8287 (tt) cc_final: 0.8041 (tt) REVERT: V 154 ASP cc_start: 0.8509 (t0) cc_final: 0.8203 (t0) REVERT: V 159 MET cc_start: 0.9095 (mmp) cc_final: 0.8790 (mmm) REVERT: V 162 ILE cc_start: 0.9123 (mt) cc_final: 0.8707 (mt) REVERT: W 65 TYR cc_start: 0.8376 (p90) cc_final: 0.8026 (p90) REVERT: W 69 MET cc_start: 0.4134 (mtp) cc_final: 0.3475 (mmm) REVERT: W 97 TYR cc_start: 0.8507 (m-10) cc_final: 0.7798 (m-80) REVERT: W 163 ASN cc_start: 0.7619 (m-40) cc_final: 0.7308 (m-40) REVERT: X 89 GLU cc_start: 0.9003 (tt0) cc_final: 0.8670 (tm-30) REVERT: X 166 PHE cc_start: 0.8051 (m-80) cc_final: 0.7803 (m-80) REVERT: Y 20 PHE cc_start: 0.8694 (m-80) cc_final: 0.8447 (m-10) REVERT: Y 36 MET cc_start: 0.7569 (ttp) cc_final: 0.7140 (mmt) REVERT: Y 50 VAL cc_start: 0.9562 (t) cc_final: 0.9330 (p) REVERT: Y 55 MET cc_start: 0.9071 (ttp) cc_final: 0.8718 (ttp) REVERT: Z 31 ASP cc_start: 0.9170 (t70) cc_final: 0.8947 (t0) REVERT: Z 42 GLN cc_start: 0.9221 (tp40) cc_final: 0.8992 (tp40) REVERT: Z 59 GLU cc_start: 0.8847 (mp0) cc_final: 0.8538 (mp0) REVERT: Z 64 ASN cc_start: 0.8992 (t0) cc_final: 0.8691 (t0) REVERT: Z 93 THR cc_start: 0.9489 (m) cc_final: 0.9180 (p) REVERT: Z 115 ILE cc_start: 0.8946 (mt) cc_final: 0.8701 (mm) REVERT: Z 119 ASP cc_start: 0.9310 (m-30) cc_final: 0.9050 (m-30) REVERT: Z 165 PHE cc_start: 0.9006 (t80) cc_final: 0.8776 (t80) REVERT: Z 175 TYR cc_start: 0.8856 (t80) cc_final: 0.8616 (t80) REVERT: Z 179 ASP cc_start: 0.9392 (m-30) cc_final: 0.9157 (m-30) REVERT: Z 187 MET cc_start: 0.8861 (ttt) cc_final: 0.8535 (mtp) REVERT: Z 196 THR cc_start: 0.9686 (p) cc_final: 0.9438 (t) REVERT: Z 264 TYR cc_start: 0.9421 (t80) cc_final: 0.8947 (t80) REVERT: a 2 THR cc_start: 0.7802 (p) cc_final: 0.7050 (t) REVERT: a 3 ILE cc_start: 0.7505 (mm) cc_final: 0.7024 (mm) REVERT: a 21 GLU cc_start: 0.8765 (pt0) cc_final: 0.7904 (tp30) REVERT: a 68 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7349 (mp) REVERT: a 74 ASN cc_start: 0.9424 (t0) cc_final: 0.9009 (p0) REVERT: a 82 PHE cc_start: 0.9103 (t80) cc_final: 0.8899 (t80) REVERT: a 104 ARG cc_start: 0.8593 (ttt90) cc_final: 0.8225 (ttp80) REVERT: a 152 ASN cc_start: 0.9332 (m-40) cc_final: 0.8940 (t0) REVERT: a 170 PHE cc_start: 0.8558 (m-10) cc_final: 0.8084 (m-80) REVERT: a 177 TYR cc_start: 0.8265 (p90) cc_final: 0.7727 (p90) outliers start: 8 outliers final: 1 residues processed: 1792 average time/residue: 0.5098 time to fit residues: 1478.8723 Evaluate side-chains 1464 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1461 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 226 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 338 optimal weight: 0.7980 chunk 277 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 407 optimal weight: 3.9990 chunk 440 optimal weight: 5.9990 chunk 362 optimal weight: 0.7980 chunk 404 optimal weight: 3.9990 chunk 138 optimal weight: 0.2980 chunk 326 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN C 25 GLN D 35 ASN E 61 GLN E 147 GLN F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 21 ASN O 25 GLN O 119 ASN ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 ASN S 46 ASN ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 145 ASN X 42 ASN ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36155 Z= 0.240 Angle : 0.734 43.131 49243 Z= 0.338 Chirality : 0.038 0.258 5448 Planarity : 0.004 0.055 6402 Dihedral : 10.756 89.027 6599 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.09 % Favored : 97.86 % Rotamer: Outliers : 0.18 % Allowed : 3.36 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.13), residues: 4448 helix: 1.37 (0.09), residues: 3340 sheet: 2.15 (0.92), residues: 28 loop : -0.80 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 47 HIS 0.005 0.002 HIS Z 117 PHE 0.033 0.002 PHE Z 143 TYR 0.028 0.002 TYR M 97 ARG 0.006 0.001 ARG D 86 *********************** 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 1733 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1727 time to evaluate : 4.063 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: A 1 MET cc_start: 0.8779 (tpp) cc_final: 0.8304 (mmt) REVERT: A 18 PHE cc_start: 0.8118 (m-80) cc_final: 0.7514 (m-80) REVERT: A 38 MET cc_start: 0.9242 (mmt) cc_final: 0.8312 (tmm) REVERT: A 39 GLU cc_start: 0.9609 (tp30) cc_final: 0.9227 (mm-30) REVERT: A 49 GLN cc_start: 0.9163 (tp40) cc_final: 0.8392 (mm-40) REVERT: A 53 ASP cc_start: 0.9243 (t0) cc_final: 0.8823 (p0) REVERT: A 62 LYS cc_start: 0.9063 (tptt) cc_final: 0.8692 (tptt) REVERT: A 63 PHE cc_start: 0.9169 (m-80) cc_final: 0.8708 (m-80) REVERT: A 98 CYS cc_start: 0.9656 (t) cc_final: 0.9189 (t) REVERT: A 122 PHE cc_start: 0.9188 (m-80) cc_final: 0.8891 (m-80) REVERT: A 167 ASP cc_start: 0.9319 (t0) cc_final: 0.8946 (t0) REVERT: B 5 PHE cc_start: 0.8832 (m-80) cc_final: 0.8501 (m-80) REVERT: B 32 LYS cc_start: 0.9006 (ttpp) cc_final: 0.8717 (tppt) REVERT: B 89 GLU cc_start: 0.9309 (pt0) cc_final: 0.8871 (tt0) REVERT: B 120 GLN cc_start: 0.8743 (mt0) cc_final: 0.8034 (tm-30) REVERT: B 136 MET cc_start: 0.9062 (mtt) cc_final: 0.6735 (mtt) REVERT: B 145 ASN cc_start: 0.8862 (t0) cc_final: 0.8275 (p0) REVERT: B 159 MET cc_start: 0.9491 (mpp) cc_final: 0.9249 (mpp) REVERT: C 65 TYR cc_start: 0.7638 (p90) cc_final: 0.7411 (p90) REVERT: C 69 MET cc_start: 0.7675 (ttm) cc_final: 0.7118 (ttm) REVERT: C 94 MET cc_start: 0.9522 (mmt) cc_final: 0.9205 (mmm) REVERT: D 81 MET cc_start: 0.7863 (tpp) cc_final: 0.7620 (ttt) REVERT: D 88 MET cc_start: 0.8437 (mmm) cc_final: 0.8149 (mmm) REVERT: D 111 CYS cc_start: 0.8454 (t) cc_final: 0.8064 (t) REVERT: D 128 SER cc_start: 0.9414 (p) cc_final: 0.9148 (p) REVERT: D 134 GLN cc_start: 0.9202 (mt0) cc_final: 0.9002 (mt0) REVERT: D 146 ASP cc_start: 0.9301 (t0) cc_final: 0.9014 (t0) REVERT: D 154 ASP cc_start: 0.7883 (t0) cc_final: 0.7626 (t0) REVERT: E 13 ASP cc_start: 0.9314 (t0) cc_final: 0.8893 (t0) REVERT: E 15 GLN cc_start: 0.8662 (mt0) cc_final: 0.8257 (mt0) REVERT: E 25 GLN cc_start: 0.9073 (mt0) cc_final: 0.8677 (mt0) REVERT: E 38 MET cc_start: 0.8769 (mmt) cc_final: 0.7937 (tmm) REVERT: E 69 MET cc_start: 0.8927 (mtp) cc_final: 0.8059 (ttm) REVERT: E 72 SER cc_start: 0.8763 (m) cc_final: 0.8443 (t) REVERT: E 73 GLN cc_start: 0.9310 (pm20) cc_final: 0.8914 (pm20) REVERT: E 74 TYR cc_start: 0.8657 (m-80) cc_final: 0.8097 (m-10) REVERT: E 99 LEU cc_start: 0.8478 (tp) cc_final: 0.8180 (tp) REVERT: E 109 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8595 (tt0) REVERT: E 115 LEU cc_start: 0.9350 (tp) cc_final: 0.9141 (tt) REVERT: E 119 ASN cc_start: 0.9186 (m-40) cc_final: 0.8955 (m110) REVERT: E 121 THR cc_start: 0.9739 (p) cc_final: 0.9437 (t) REVERT: E 123 ASP cc_start: 0.8946 (m-30) cc_final: 0.8577 (t0) REVERT: E 165 TYR cc_start: 0.8873 (m-10) cc_final: 0.8631 (m-10) REVERT: E 167 ASP cc_start: 0.9290 (t0) cc_final: 0.8613 (t0) REVERT: F 21 ASN cc_start: 0.8496 (m-40) cc_final: 0.7442 (t0) REVERT: F 25 ASP cc_start: 0.8986 (m-30) cc_final: 0.8395 (m-30) REVERT: F 29 ASN cc_start: 0.9583 (m-40) cc_final: 0.9178 (m-40) REVERT: F 30 LEU cc_start: 0.9470 (mm) cc_final: 0.9214 (tp) REVERT: F 32 LYS cc_start: 0.9186 (pttm) cc_final: 0.8847 (pttm) REVERT: F 35 ASN cc_start: 0.9350 (m-40) cc_final: 0.9087 (m-40) REVERT: F 62 GLU cc_start: 0.9486 (tt0) cc_final: 0.9188 (tm-30) REVERT: F 76 TYR cc_start: 0.8972 (t80) cc_final: 0.7753 (t80) REVERT: F 81 MET cc_start: 0.9005 (tpp) cc_final: 0.8764 (tpp) REVERT: F 88 MET cc_start: 0.9354 (tpp) cc_final: 0.8998 (tpp) REVERT: F 103 ASP cc_start: 0.8806 (t0) cc_final: 0.8483 (t70) REVERT: F 137 LYS cc_start: 0.9375 (ttpt) cc_final: 0.9056 (ttpt) REVERT: F 146 ASP cc_start: 0.8730 (t0) cc_final: 0.8450 (t0) REVERT: F 161 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9075 (tp30) REVERT: F 165 TYR cc_start: 0.9575 (m-80) cc_final: 0.9103 (m-10) REVERT: G 5 ILE cc_start: 0.9180 (mp) cc_final: 0.8941 (tt) REVERT: G 19 LEU cc_start: 0.8674 (mm) cc_final: 0.8369 (mm) REVERT: G 28 ASP cc_start: 0.8910 (t0) cc_final: 0.8693 (t70) REVERT: G 62 LYS cc_start: 0.9261 (tptm) cc_final: 0.9017 (tppt) REVERT: G 70 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8134 (pp30) REVERT: G 74 TYR cc_start: 0.9117 (m-80) cc_final: 0.8804 (m-10) REVERT: G 79 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8717 (pp20) REVERT: G 97 TYR cc_start: 0.9417 (m-10) cc_final: 0.9010 (m-10) REVERT: G 99 LEU cc_start: 0.9030 (tp) cc_final: 0.8609 (tp) REVERT: G 119 ASN cc_start: 0.9267 (m110) cc_final: 0.8843 (m-40) REVERT: G 122 PHE cc_start: 0.9181 (m-80) cc_final: 0.8860 (m-10) REVERT: G 123 ASP cc_start: 0.8789 (t0) cc_final: 0.8469 (t70) REVERT: G 124 LEU cc_start: 0.9125 (mt) cc_final: 0.8885 (mt) REVERT: G 129 TYR cc_start: 0.9160 (m-80) cc_final: 0.8178 (m-80) REVERT: G 163 ASN cc_start: 0.9316 (m-40) cc_final: 0.8959 (m-40) REVERT: G 167 ASP cc_start: 0.9091 (t0) cc_final: 0.8721 (t0) REVERT: H 1 MET cc_start: 0.8640 (mtt) cc_final: 0.8290 (mpp) REVERT: H 3 ASP cc_start: 0.9286 (p0) cc_final: 0.8835 (p0) REVERT: H 15 ARG cc_start: 0.7808 (mmm160) cc_final: 0.7308 (mtm-85) REVERT: H 17 GLU cc_start: 0.9466 (pm20) cc_final: 0.9167 (pm20) REVERT: H 87 ASP cc_start: 0.9452 (m-30) cc_final: 0.8720 (m-30) REVERT: H 117 GLU cc_start: 0.9213 (tp30) cc_final: 0.8945 (tp30) REVERT: H 143 ILE cc_start: 0.8971 (mm) cc_final: 0.8745 (tp) REVERT: I 51 LEU cc_start: 0.9297 (mt) cc_final: 0.8966 (mt) REVERT: I 60 TYR cc_start: 0.8354 (m-10) cc_final: 0.8096 (m-80) REVERT: I 62 LYS cc_start: 0.9357 (tptm) cc_final: 0.8770 (tptt) REVERT: I 94 MET cc_start: 0.8987 (mmm) cc_final: 0.8661 (tpp) REVERT: I 110 TYR cc_start: 0.9119 (m-80) cc_final: 0.8725 (m-10) REVERT: I 115 LEU cc_start: 0.9243 (tp) cc_final: 0.8695 (tt) REVERT: I 118 ILE cc_start: 0.9425 (mm) cc_final: 0.9210 (pt) REVERT: I 119 ASN cc_start: 0.9465 (m110) cc_final: 0.9022 (m110) REVERT: I 140 HIS cc_start: 0.9398 (p90) cc_final: 0.9178 (p-80) REVERT: I 170 ILE cc_start: 0.9657 (tt) cc_final: 0.9215 (pt) REVERT: J 24 PHE cc_start: 0.8221 (m-80) cc_final: 0.8019 (m-80) REVERT: J 35 ASN cc_start: 0.9126 (m110) cc_final: 0.8234 (t0) REVERT: J 97 TYR cc_start: 0.8995 (m-10) cc_final: 0.8372 (m-10) REVERT: J 112 LEU cc_start: 0.9342 (mp) cc_final: 0.8939 (mp) REVERT: J 141 ILE cc_start: 0.9217 (tp) cc_final: 0.8931 (tp) REVERT: J 145 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7702 (t0) REVERT: J 159 MET cc_start: 0.8729 (mmp) cc_final: 0.8457 (mmm) REVERT: J 167 ASP cc_start: 0.8835 (m-30) cc_final: 0.8629 (t0) REVERT: K 18 PHE cc_start: 0.8915 (m-80) cc_final: 0.8516 (m-10) REVERT: K 21 ASN cc_start: 0.8454 (p0) cc_final: 0.8194 (t0) REVERT: K 57 GLN cc_start: 0.9025 (pp30) cc_final: 0.8682 (mm-40) REVERT: K 97 TYR cc_start: 0.8468 (m-10) cc_final: 0.7827 (m-80) REVERT: K 140 HIS cc_start: 0.8742 (p-80) cc_final: 0.8430 (p90) REVERT: L 2 LEU cc_start: 0.9610 (mt) cc_final: 0.9195 (mt) REVERT: L 13 ASP cc_start: 0.8816 (t70) cc_final: 0.8586 (t0) REVERT: L 41 VAL cc_start: 0.9562 (m) cc_final: 0.9349 (p) REVERT: L 80 ARG cc_start: 0.8957 (mtm-85) cc_final: 0.8735 (mtm-85) REVERT: L 87 ASP cc_start: 0.9082 (m-30) cc_final: 0.8822 (m-30) REVERT: L 88 MET cc_start: 0.8241 (mtm) cc_final: 0.7679 (mtp) REVERT: L 89 GLU cc_start: 0.9165 (pp20) cc_final: 0.8588 (tm-30) REVERT: L 90 ILE cc_start: 0.8985 (mt) cc_final: 0.8315 (mm) REVERT: L 113 ASN cc_start: 0.9411 (t0) cc_final: 0.8626 (t0) REVERT: L 137 LYS cc_start: 0.9362 (tttt) cc_final: 0.8899 (ttmt) REVERT: L 159 MET cc_start: 0.9206 (mmp) cc_final: 0.8941 (mmt) REVERT: L 161 GLU cc_start: 0.9092 (tt0) cc_final: 0.8670 (tp30) REVERT: M 33 ARG cc_start: 0.8988 (tpt-90) cc_final: 0.8533 (ttt180) REVERT: M 81 LYS cc_start: 0.8932 (tmtt) cc_final: 0.8672 (mtpp) REVERT: M 107 MET cc_start: 0.8702 (mmm) cc_final: 0.8153 (mmm) REVERT: M 129 TYR cc_start: 0.8756 (m-80) cc_final: 0.8501 (m-80) REVERT: M 135 TYR cc_start: 0.9260 (t80) cc_final: 0.9015 (t80) REVERT: M 161 GLU cc_start: 0.9431 (tt0) cc_final: 0.9193 (mt-10) REVERT: M 171 ASN cc_start: 0.8455 (p0) cc_final: 0.8131 (p0) REVERT: N 24 PHE cc_start: 0.8750 (m-80) cc_final: 0.8535 (m-80) REVERT: N 35 ASN cc_start: 0.9482 (m-40) cc_final: 0.9083 (t0) REVERT: N 62 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8745 (tm-30) REVERT: N 65 GLN cc_start: 0.8585 (mp10) cc_final: 0.8131 (mp10) REVERT: N 87 ASP cc_start: 0.9272 (m-30) cc_final: 0.8978 (m-30) REVERT: N 88 MET cc_start: 0.8889 (ttp) cc_final: 0.7524 (tpt) REVERT: N 103 ASP cc_start: 0.7970 (t0) cc_final: 0.7402 (t0) REVERT: N 107 LEU cc_start: 0.9470 (tp) cc_final: 0.9137 (tp) REVERT: N 115 LEU cc_start: 0.9387 (tp) cc_final: 0.9186 (tt) REVERT: N 119 TYR cc_start: 0.9460 (m-10) cc_final: 0.8983 (m-10) REVERT: N 136 MET cc_start: 0.8929 (mtm) cc_final: 0.7810 (mtm) REVERT: N 141 ILE cc_start: 0.8947 (tp) cc_final: 0.8734 (tp) REVERT: N 159 MET cc_start: 0.9326 (mmt) cc_final: 0.9017 (mmm) REVERT: O 13 ASP cc_start: 0.9308 (t70) cc_final: 0.9044 (t0) REVERT: O 19 LEU cc_start: 0.8453 (mm) cc_final: 0.8171 (mm) REVERT: O 98 CYS cc_start: 0.9151 (p) cc_final: 0.8911 (m) REVERT: O 99 LEU cc_start: 0.9349 (mt) cc_final: 0.9039 (tp) REVERT: O 104 THR cc_start: 0.9116 (p) cc_final: 0.8680 (p) REVERT: O 129 TYR cc_start: 0.9053 (m-80) cc_final: 0.8423 (m-80) REVERT: O 131 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8964 (pt0) REVERT: P 1 MET cc_start: 0.6893 (ptt) cc_final: 0.6316 (ptt) REVERT: P 5 PHE cc_start: 0.9210 (m-10) cc_final: 0.8814 (m-10) REVERT: P 9 VAL cc_start: 0.9754 (t) cc_final: 0.9447 (p) REVERT: P 23 GLN cc_start: 0.8529 (mt0) cc_final: 0.8326 (mt0) REVERT: P 81 MET cc_start: 0.8542 (tpp) cc_final: 0.8277 (tpp) REVERT: P 88 MET cc_start: 0.8773 (mmm) cc_final: 0.8568 (mmm) REVERT: P 94 TYR cc_start: 0.9101 (m-80) cc_final: 0.8567 (m-80) REVERT: P 97 TYR cc_start: 0.8971 (m-10) cc_final: 0.8115 (m-80) REVERT: P 113 ASN cc_start: 0.8750 (t0) cc_final: 0.8534 (t0) REVERT: P 124 THR cc_start: 0.9045 (m) cc_final: 0.8767 (p) REVERT: P 159 MET cc_start: 0.9109 (mmm) cc_final: 0.8051 (ppp) REVERT: Q 2 LYS cc_start: 0.8730 (mttm) cc_final: 0.8348 (mmtp) REVERT: Q 25 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8197 (mm-40) REVERT: Q 30 ARG cc_start: 0.7542 (tpt-90) cc_final: 0.7330 (tpt-90) REVERT: Q 37 SER cc_start: 0.8309 (m) cc_final: 0.7620 (p) REVERT: Q 39 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7682 (pt0) REVERT: Q 62 LYS cc_start: 0.6344 (tptm) cc_final: 0.6062 (ttmt) REVERT: Q 69 MET cc_start: 0.5119 (ptm) cc_final: 0.4742 (ptm) REVERT: Q 98 CYS cc_start: 0.8622 (m) cc_final: 0.8366 (m) REVERT: R 38 LEU cc_start: 0.8279 (mt) cc_final: 0.7540 (mp) REVERT: R 85 LEU cc_start: 0.9689 (mt) cc_final: 0.9342 (tp) REVERT: R 87 ASP cc_start: 0.8091 (m-30) cc_final: 0.7793 (m-30) REVERT: R 88 MET cc_start: 0.9563 (mmm) cc_final: 0.9198 (mtm) REVERT: R 103 ASP cc_start: 0.7178 (t0) cc_final: 0.6950 (t70) REVERT: R 111 CYS cc_start: 0.8323 (t) cc_final: 0.7916 (t) REVERT: R 128 SER cc_start: 0.8460 (m) cc_final: 0.8165 (m) REVERT: R 134 GLN cc_start: 0.8619 (mm110) cc_final: 0.8006 (mm-40) REVERT: R 136 MET cc_start: 0.8781 (ttp) cc_final: 0.8242 (tmm) REVERT: R 159 MET cc_start: 0.8482 (mmp) cc_final: 0.8116 (ptt) REVERT: S 28 ASP cc_start: 0.8888 (t0) cc_final: 0.8680 (t0) REVERT: S 44 LEU cc_start: 0.9687 (mt) cc_final: 0.9035 (tp) REVERT: S 49 GLN cc_start: 0.9389 (tp-100) cc_final: 0.8680 (pm20) REVERT: S 63 PHE cc_start: 0.8697 (m-80) cc_final: 0.8207 (m-80) REVERT: S 73 GLN cc_start: 0.8840 (pt0) cc_final: 0.8462 (pm20) REVERT: S 74 TYR cc_start: 0.9281 (m-80) cc_final: 0.8625 (m-80) REVERT: S 79 GLU cc_start: 0.8418 (mp0) cc_final: 0.8083 (tm-30) REVERT: S 84 CYS cc_start: 0.9019 (t) cc_final: 0.8809 (t) REVERT: S 90 TYR cc_start: 0.9040 (m-10) cc_final: 0.8657 (m-10) REVERT: S 97 TYR cc_start: 0.9412 (m-80) cc_final: 0.8702 (m-80) REVERT: S 133 LEU cc_start: 0.9002 (mt) cc_final: 0.8768 (mt) REVERT: S 137 LYS cc_start: 0.9259 (ttpt) cc_final: 0.8993 (tptt) REVERT: T 1 MET cc_start: 0.7773 (ttt) cc_final: 0.6843 (tmm) REVERT: T 15 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7211 (mmm160) REVERT: T 19 LEU cc_start: 0.8083 (mt) cc_final: 0.7435 (mt) REVERT: T 23 GLN cc_start: 0.8317 (mt0) cc_final: 0.7790 (mp10) REVERT: T 47 ASN cc_start: 0.8000 (t0) cc_final: 0.7703 (t0) REVERT: T 158 LEU cc_start: 0.8163 (tt) cc_final: 0.7855 (tt) REVERT: U 65 TYR cc_start: 0.9121 (p90) cc_final: 0.8877 (p90) REVERT: U 69 MET cc_start: 0.7785 (mtt) cc_final: 0.6912 (tpp) REVERT: U 109 GLU cc_start: 0.9271 (tm-30) cc_final: 0.8867 (tm-30) REVERT: U 115 LEU cc_start: 0.8888 (tp) cc_final: 0.8584 (tp) REVERT: U 117 GLU cc_start: 0.9049 (tt0) cc_final: 0.8827 (mp0) REVERT: U 123 ASP cc_start: 0.9296 (t0) cc_final: 0.9080 (t70) REVERT: U 171 ASN cc_start: 0.9010 (t0) cc_final: 0.8800 (t0) REVERT: V 11 GLN cc_start: 0.8975 (tt0) cc_final: 0.8391 (tp40) REVERT: V 60 PHE cc_start: 0.8959 (m-80) cc_final: 0.8609 (m-80) REVERT: V 62 GLU cc_start: 0.9337 (tm-30) cc_final: 0.9110 (tm-30) REVERT: V 68 GLN cc_start: 0.9033 (pt0) cc_final: 0.8719 (pt0) REVERT: V 78 ASN cc_start: 0.7869 (t0) cc_final: 0.7483 (t0) REVERT: V 81 MET cc_start: 0.8877 (tpp) cc_final: 0.8286 (tpp) REVERT: V 108 ASP cc_start: 0.9164 (m-30) cc_final: 0.8954 (t0) REVERT: V 113 ASN cc_start: 0.8453 (t0) cc_final: 0.8048 (t0) REVERT: V 137 LYS cc_start: 0.9233 (tttt) cc_final: 0.8590 (tttm) REVERT: V 150 ILE cc_start: 0.8351 (tt) cc_final: 0.7818 (pt) REVERT: V 154 ASP cc_start: 0.8504 (t0) cc_final: 0.8287 (t0) REVERT: V 159 MET cc_start: 0.9026 (mmp) cc_final: 0.8589 (tmm) REVERT: V 162 ILE cc_start: 0.9132 (mt) cc_final: 0.8707 (mt) REVERT: V 166 PHE cc_start: 0.9242 (m-80) cc_final: 0.9008 (m-80) REVERT: W 42 ARG cc_start: 0.7779 (ttm170) cc_final: 0.6618 (tpt170) REVERT: W 65 TYR cc_start: 0.8460 (p90) cc_final: 0.8143 (p90) REVERT: W 69 MET cc_start: 0.4687 (mtp) cc_final: 0.4059 (mmm) REVERT: W 94 MET cc_start: 0.8344 (mmp) cc_final: 0.7994 (mmp) REVERT: W 97 TYR cc_start: 0.8541 (m-10) cc_final: 0.7928 (m-80) REVERT: W 100 VAL cc_start: 0.9208 (t) cc_final: 0.8822 (m) REVERT: W 163 ASN cc_start: 0.7531 (m-40) cc_final: 0.7308 (m-40) REVERT: X 88 MET cc_start: 0.9258 (ttm) cc_final: 0.8993 (ttt) REVERT: X 89 GLU cc_start: 0.8975 (tt0) cc_final: 0.8563 (tm-30) REVERT: X 136 MET cc_start: 0.7940 (mmt) cc_final: 0.7682 (mmm) REVERT: X 150 ILE cc_start: 0.6910 (tt) cc_final: 0.6631 (tt) REVERT: X 166 PHE cc_start: 0.7874 (m-80) cc_final: 0.7587 (m-80) REVERT: Y 20 PHE cc_start: 0.8612 (m-80) cc_final: 0.8183 (m-80) REVERT: Y 28 ARG cc_start: 0.9236 (ttp-170) cc_final: 0.8651 (ttm170) REVERT: Y 36 MET cc_start: 0.7595 (ttp) cc_final: 0.7079 (mmt) REVERT: Y 47 PHE cc_start: 0.8642 (m-80) cc_final: 0.8384 (m-80) REVERT: Y 50 VAL cc_start: 0.9600 (t) cc_final: 0.9364 (p) REVERT: Z 31 ASP cc_start: 0.9254 (t70) cc_final: 0.9053 (t0) REVERT: Z 59 GLU cc_start: 0.9078 (mp0) cc_final: 0.8577 (pt0) REVERT: Z 115 ILE cc_start: 0.8917 (mt) cc_final: 0.8704 (mm) REVERT: Z 119 ASP cc_start: 0.9458 (m-30) cc_final: 0.9024 (m-30) REVERT: Z 143 PHE cc_start: 0.8861 (m-10) cc_final: 0.8556 (m-80) REVERT: Z 179 ASP cc_start: 0.9293 (m-30) cc_final: 0.8913 (m-30) REVERT: Z 187 MET cc_start: 0.8519 (ttt) cc_final: 0.8155 (mtp) REVERT: Z 196 THR cc_start: 0.9684 (p) cc_final: 0.9475 (t) REVERT: a 3 ILE cc_start: 0.7537 (mm) cc_final: 0.7174 (mm) REVERT: a 16 ARG cc_start: 0.8949 (ttp80) cc_final: 0.8155 (ttp80) REVERT: a 65 GLN cc_start: 0.7918 (tt0) cc_final: 0.7448 (tm-30) REVERT: a 74 ASN cc_start: 0.9414 (t0) cc_final: 0.8906 (p0) REVERT: a 104 ARG cc_start: 0.8544 (ttt90) cc_final: 0.8250 (ttp80) REVERT: a 152 ASN cc_start: 0.9284 (m-40) cc_final: 0.8897 (t0) outliers start: 6 outliers final: 0 residues processed: 1728 average time/residue: 0.4757 time to fit residues: 1327.2325 Evaluate side-chains 1388 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1387 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 402 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 273 optimal weight: 1.9990 chunk 409 optimal weight: 7.9990 chunk 433 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 387 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN E 61 GLN ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN Q 139 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 ASN T 78 ASN ** U 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 145 ASN Z 92 GLN ** Z 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 36155 Z= 0.249 Angle : 0.732 43.081 49243 Z= 0.338 Chirality : 0.038 0.219 5448 Planarity : 0.004 0.055 6402 Dihedral : 10.829 89.446 6599 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.41 % Favored : 97.50 % Rotamer: Outliers : 0.18 % Allowed : 2.62 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.13), residues: 4448 helix: 1.43 (0.09), residues: 3298 sheet: 2.29 (0.81), residues: 28 loop : -0.82 (0.21), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP a 47 HIS 0.006 0.002 HIS Z 117 PHE 0.022 0.002 PHE R 60 TYR 0.043 0.002 TYR M 97 ARG 0.006 0.001 ARG Y 64 *********************** 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 1653 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1647 time to evaluate : 3.809 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: A 2 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7462 (ttpt) REVERT: A 18 PHE cc_start: 0.8188 (m-80) cc_final: 0.7612 (m-80) REVERT: A 38 MET cc_start: 0.9222 (mmt) cc_final: 0.8223 (tmm) REVERT: A 39 GLU cc_start: 0.9598 (tp30) cc_final: 0.9184 (mm-30) REVERT: A 49 GLN cc_start: 0.8991 (tp40) cc_final: 0.8433 (mm-40) REVERT: A 53 ASP cc_start: 0.9134 (t0) cc_final: 0.8803 (p0) REVERT: A 62 LYS cc_start: 0.9323 (tptt) cc_final: 0.9029 (tptt) REVERT: A 63 PHE cc_start: 0.9189 (m-80) cc_final: 0.8972 (m-10) REVERT: A 90 TYR cc_start: 0.9339 (m-10) cc_final: 0.8938 (m-80) REVERT: A 98 CYS cc_start: 0.9580 (t) cc_final: 0.8869 (t) REVERT: A 122 PHE cc_start: 0.9217 (m-80) cc_final: 0.8939 (m-80) REVERT: A 165 TYR cc_start: 0.8900 (m-80) cc_final: 0.8365 (m-80) REVERT: A 167 ASP cc_start: 0.9348 (t0) cc_final: 0.8955 (t0) REVERT: B 32 LYS cc_start: 0.9018 (ttpp) cc_final: 0.8730 (tppt) REVERT: B 89 GLU cc_start: 0.9397 (pt0) cc_final: 0.8900 (tt0) REVERT: B 120 GLN cc_start: 0.8736 (mt0) cc_final: 0.8029 (tm-30) REVERT: B 136 MET cc_start: 0.8776 (mtt) cc_final: 0.7819 (mtt) REVERT: B 145 ASN cc_start: 0.8801 (t0) cc_final: 0.8179 (p0) REVERT: C 63 PHE cc_start: 0.9079 (m-10) cc_final: 0.8709 (m-10) REVERT: C 69 MET cc_start: 0.7668 (ttm) cc_final: 0.7153 (ttm) REVERT: C 94 MET cc_start: 0.9593 (mmt) cc_final: 0.9197 (mmm) REVERT: C 109 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8414 (tp30) REVERT: D 81 MET cc_start: 0.7999 (tpp) cc_final: 0.7747 (ttt) REVERT: D 88 MET cc_start: 0.8560 (mmm) cc_final: 0.8261 (mmm) REVERT: D 97 TYR cc_start: 0.9121 (m-10) cc_final: 0.8455 (m-80) REVERT: D 111 CYS cc_start: 0.8462 (t) cc_final: 0.8065 (t) REVERT: D 128 SER cc_start: 0.9411 (p) cc_final: 0.9137 (p) REVERT: D 146 ASP cc_start: 0.9380 (t0) cc_final: 0.9167 (t0) REVERT: D 154 ASP cc_start: 0.7841 (t0) cc_final: 0.7567 (t0) REVERT: E 15 GLN cc_start: 0.8216 (mt0) cc_final: 0.7890 (mt0) REVERT: E 25 GLN cc_start: 0.8971 (mt0) cc_final: 0.8631 (mt0) REVERT: E 38 MET cc_start: 0.8766 (mmt) cc_final: 0.7954 (tmm) REVERT: E 72 SER cc_start: 0.8769 (m) cc_final: 0.8279 (t) REVERT: E 86 ARG cc_start: 0.8711 (ttp80) cc_final: 0.8389 (tmm-80) REVERT: E 109 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8621 (tt0) REVERT: E 115 LEU cc_start: 0.9401 (tp) cc_final: 0.9190 (tt) REVERT: E 121 THR cc_start: 0.9752 (p) cc_final: 0.9538 (t) REVERT: E 123 ASP cc_start: 0.8983 (m-30) cc_final: 0.8567 (t0) REVERT: E 167 ASP cc_start: 0.9467 (t0) cc_final: 0.8596 (t0) REVERT: E 171 ASN cc_start: 0.9196 (p0) cc_final: 0.8928 (p0) REVERT: F 1 MET cc_start: 0.8754 (tpp) cc_final: 0.8156 (tpp) REVERT: F 3 ASP cc_start: 0.9268 (p0) cc_final: 0.9034 (p0) REVERT: F 21 ASN cc_start: 0.8497 (m-40) cc_final: 0.7433 (t0) REVERT: F 35 ASN cc_start: 0.9390 (m-40) cc_final: 0.9074 (m-40) REVERT: F 76 TYR cc_start: 0.9001 (t80) cc_final: 0.7896 (t80) REVERT: F 81 MET cc_start: 0.8927 (tpp) cc_final: 0.8691 (tpt) REVERT: F 137 LYS cc_start: 0.9407 (ttpt) cc_final: 0.9093 (ttpt) REVERT: F 146 ASP cc_start: 0.8912 (t0) cc_final: 0.8615 (t0) REVERT: F 159 MET cc_start: 0.8818 (mmt) cc_final: 0.8475 (mmm) REVERT: F 161 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9080 (tp30) REVERT: F 165 TYR cc_start: 0.9568 (m-80) cc_final: 0.8957 (m-10) REVERT: G 5 ILE cc_start: 0.9183 (mp) cc_final: 0.8892 (tt) REVERT: G 28 ASP cc_start: 0.8759 (t0) cc_final: 0.8553 (t70) REVERT: G 74 TYR cc_start: 0.9156 (m-80) cc_final: 0.8907 (m-10) REVERT: G 79 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8723 (pp20) REVERT: G 97 TYR cc_start: 0.9426 (m-10) cc_final: 0.8979 (m-10) REVERT: G 99 LEU cc_start: 0.9119 (tp) cc_final: 0.8669 (tp) REVERT: G 119 ASN cc_start: 0.9505 (m-40) cc_final: 0.9186 (m-40) REVERT: G 123 ASP cc_start: 0.8848 (t0) cc_final: 0.8423 (t0) REVERT: G 124 LEU cc_start: 0.9164 (mt) cc_final: 0.8825 (mt) REVERT: G 163 ASN cc_start: 0.9411 (m-40) cc_final: 0.9016 (m-40) REVERT: H 1 MET cc_start: 0.8694 (mtt) cc_final: 0.8324 (mpp) REVERT: H 3 ASP cc_start: 0.9320 (p0) cc_final: 0.8933 (p0) REVERT: H 117 GLU cc_start: 0.9300 (tp30) cc_final: 0.9027 (tp30) REVERT: I 47 ASN cc_start: 0.8049 (p0) cc_final: 0.7732 (p0) REVERT: I 51 LEU cc_start: 0.9262 (mt) cc_final: 0.8994 (mt) REVERT: I 94 MET cc_start: 0.8949 (mmm) cc_final: 0.8713 (tpp) REVERT: I 111 LEU cc_start: 0.9516 (tp) cc_final: 0.9314 (tp) REVERT: I 115 LEU cc_start: 0.9034 (tp) cc_final: 0.8810 (tp) REVERT: I 119 ASN cc_start: 0.9405 (m110) cc_final: 0.9156 (m110) REVERT: I 133 LEU cc_start: 0.9534 (mt) cc_final: 0.9323 (mt) REVERT: J 17 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8622 (mp0) REVERT: J 35 ASN cc_start: 0.9166 (m110) cc_final: 0.8302 (t0) REVERT: J 112 LEU cc_start: 0.9395 (mp) cc_final: 0.8888 (mm) REVERT: K 21 ASN cc_start: 0.8452 (p0) cc_final: 0.8225 (t0) REVERT: K 57 GLN cc_start: 0.8990 (pp30) cc_final: 0.8612 (mm-40) REVERT: L 2 LEU cc_start: 0.9624 (mt) cc_final: 0.9154 (mt) REVERT: L 7 LYS cc_start: 0.9344 (ttpp) cc_final: 0.9021 (ptmm) REVERT: L 13 ASP cc_start: 0.8872 (t70) cc_final: 0.8521 (t0) REVERT: L 33 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8840 (mp0) REVERT: L 80 ARG cc_start: 0.8976 (mtm-85) cc_final: 0.8752 (mtm-85) REVERT: L 89 GLU cc_start: 0.9059 (pp20) cc_final: 0.8539 (tm-30) REVERT: L 90 ILE cc_start: 0.8832 (mt) cc_final: 0.8165 (mm) REVERT: L 103 ASP cc_start: 0.9428 (m-30) cc_final: 0.9095 (m-30) REVERT: L 113 ASN cc_start: 0.9429 (t0) cc_final: 0.8656 (t0) REVERT: L 137 LYS cc_start: 0.9270 (tttt) cc_final: 0.8818 (ttmt) REVERT: L 146 ASP cc_start: 0.9232 (t0) cc_final: 0.8979 (t0) REVERT: L 161 GLU cc_start: 0.9070 (tt0) cc_final: 0.8639 (tp30) REVERT: M 33 ARG cc_start: 0.9013 (tpt-90) cc_final: 0.8512 (ttt180) REVERT: M 81 LYS cc_start: 0.8975 (tmtt) cc_final: 0.8751 (mtpp) REVERT: M 99 LEU cc_start: 0.8974 (mt) cc_final: 0.8736 (mt) REVERT: M 107 MET cc_start: 0.8575 (mmm) cc_final: 0.8086 (mmm) REVERT: M 118 ILE cc_start: 0.9314 (tp) cc_final: 0.9058 (tp) REVERT: M 129 TYR cc_start: 0.8682 (m-80) cc_final: 0.8381 (m-80) REVERT: M 133 LEU cc_start: 0.9771 (mm) cc_final: 0.9041 (tt) REVERT: M 161 GLU cc_start: 0.9416 (tt0) cc_final: 0.9159 (mt-10) REVERT: M 171 ASN cc_start: 0.8553 (p0) cc_final: 0.8144 (p0) REVERT: N 35 ASN cc_start: 0.9484 (m-40) cc_final: 0.9054 (t0) REVERT: N 62 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8790 (tm-30) REVERT: N 65 GLN cc_start: 0.8526 (mp10) cc_final: 0.8007 (mp10) REVERT: N 87 ASP cc_start: 0.8926 (m-30) cc_final: 0.8647 (m-30) REVERT: N 88 MET cc_start: 0.8745 (ttp) cc_final: 0.7530 (tpt) REVERT: N 95 VAL cc_start: 0.9788 (t) cc_final: 0.9376 (p) REVERT: N 103 ASP cc_start: 0.8256 (t0) cc_final: 0.7867 (t0) REVERT: N 115 LEU cc_start: 0.9375 (tp) cc_final: 0.9169 (tt) REVERT: N 119 TYR cc_start: 0.9344 (m-10) cc_final: 0.8867 (m-10) REVERT: N 136 MET cc_start: 0.8939 (mtm) cc_final: 0.7856 (mtm) REVERT: N 159 MET cc_start: 0.9346 (mmt) cc_final: 0.9088 (mmt) REVERT: O 19 LEU cc_start: 0.8438 (mm) cc_final: 0.8211 (mm) REVERT: O 99 LEU cc_start: 0.9352 (mt) cc_final: 0.9036 (tp) REVERT: O 104 THR cc_start: 0.9121 (p) cc_final: 0.8840 (p) REVERT: O 111 LEU cc_start: 0.9289 (tp) cc_final: 0.8991 (tp) REVERT: O 129 TYR cc_start: 0.9062 (m-80) cc_final: 0.8379 (m-80) REVERT: O 131 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8945 (pt0) REVERT: O 165 TYR cc_start: 0.8719 (m-80) cc_final: 0.8048 (m-80) REVERT: P 5 PHE cc_start: 0.9246 (m-10) cc_final: 0.8960 (m-10) REVERT: P 9 VAL cc_start: 0.9781 (t) cc_final: 0.9438 (p) REVERT: P 23 GLN cc_start: 0.8550 (mt0) cc_final: 0.8297 (mt0) REVERT: P 97 TYR cc_start: 0.8988 (m-10) cc_final: 0.8586 (m-10) REVERT: P 113 ASN cc_start: 0.8675 (t0) cc_final: 0.8434 (t0) REVERT: P 122 LEU cc_start: 0.8842 (mm) cc_final: 0.8598 (mm) REVERT: P 124 THR cc_start: 0.9068 (m) cc_final: 0.8742 (p) REVERT: P 159 MET cc_start: 0.9184 (mmm) cc_final: 0.8750 (mmm) REVERT: Q 25 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8417 (mm-40) REVERT: Q 39 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7639 (pt0) REVERT: Q 108 ASP cc_start: 0.9229 (m-30) cc_final: 0.8945 (m-30) REVERT: Q 123 ASP cc_start: 0.9395 (t70) cc_final: 0.9114 (m-30) REVERT: R 29 ASN cc_start: 0.8063 (t0) cc_final: 0.7389 (m110) REVERT: R 30 LEU cc_start: 0.5978 (mm) cc_final: 0.5700 (mm) REVERT: R 33 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6479 (pm20) REVERT: R 38 LEU cc_start: 0.8585 (mt) cc_final: 0.8144 (mp) REVERT: R 80 ARG cc_start: 0.8614 (mtm-85) cc_final: 0.8220 (mtm-85) REVERT: R 85 LEU cc_start: 0.9705 (mt) cc_final: 0.9396 (tp) REVERT: R 87 ASP cc_start: 0.8115 (m-30) cc_final: 0.7616 (m-30) REVERT: R 88 MET cc_start: 0.9549 (mmm) cc_final: 0.9225 (mtm) REVERT: R 111 CYS cc_start: 0.8602 (t) cc_final: 0.8202 (t) REVERT: R 128 SER cc_start: 0.8490 (m) cc_final: 0.8203 (m) REVERT: R 136 MET cc_start: 0.8724 (ttp) cc_final: 0.8172 (tmm) REVERT: R 159 MET cc_start: 0.8545 (mmp) cc_final: 0.7793 (ptt) REVERT: S 32 LYS cc_start: 0.8170 (mmtm) cc_final: 0.7963 (mmtm) REVERT: S 49 GLN cc_start: 0.9388 (tp-100) cc_final: 0.8757 (pm20) REVERT: S 73 GLN cc_start: 0.8889 (pt0) cc_final: 0.8465 (pm20) REVERT: S 74 TYR cc_start: 0.9251 (m-80) cc_final: 0.8632 (m-80) REVERT: S 79 GLU cc_start: 0.8417 (mp0) cc_final: 0.8074 (tm-30) REVERT: S 84 CYS cc_start: 0.9102 (t) cc_final: 0.8824 (t) REVERT: S 97 TYR cc_start: 0.9415 (m-80) cc_final: 0.8748 (m-80) REVERT: S 137 LYS cc_start: 0.9254 (ttpt) cc_final: 0.8973 (tptt) REVERT: S 139 ASN cc_start: 0.9167 (m110) cc_final: 0.8779 (m110) REVERT: T 1 MET cc_start: 0.7937 (ttm) cc_final: 0.7157 (tmm) REVERT: T 9 VAL cc_start: 0.9188 (t) cc_final: 0.8871 (p) REVERT: T 13 ASP cc_start: 0.8693 (t0) cc_final: 0.8374 (t0) REVERT: T 15 ARG cc_start: 0.8215 (mtp85) cc_final: 0.7328 (mmm160) REVERT: T 19 LEU cc_start: 0.8045 (mt) cc_final: 0.7393 (mt) REVERT: T 23 GLN cc_start: 0.8316 (mt0) cc_final: 0.7775 (mp10) REVERT: T 47 ASN cc_start: 0.7720 (t0) cc_final: 0.7328 (t0) REVERT: T 93 ARG cc_start: 0.8587 (ttp-170) cc_final: 0.6899 (tpp80) REVERT: U 28 ASP cc_start: 0.9167 (t70) cc_final: 0.8922 (t0) REVERT: U 65 TYR cc_start: 0.9214 (p90) cc_final: 0.8861 (p90) REVERT: U 109 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8658 (tm-30) REVERT: U 115 LEU cc_start: 0.8923 (tp) cc_final: 0.8529 (tp) REVERT: U 117 GLU cc_start: 0.9049 (tt0) cc_final: 0.8849 (mp0) REVERT: U 123 ASP cc_start: 0.9434 (t0) cc_final: 0.9116 (t0) REVERT: V 11 GLN cc_start: 0.8937 (tt0) cc_final: 0.8359 (tp40) REVERT: V 60 PHE cc_start: 0.8974 (m-80) cc_final: 0.8653 (m-80) REVERT: V 62 GLU cc_start: 0.9392 (tm-30) cc_final: 0.9147 (tm-30) REVERT: V 67 ILE cc_start: 0.8992 (pt) cc_final: 0.8779 (mt) REVERT: V 68 GLN cc_start: 0.9040 (pt0) cc_final: 0.8801 (pt0) REVERT: V 78 ASN cc_start: 0.7850 (t0) cc_final: 0.7571 (t0) REVERT: V 81 MET cc_start: 0.8784 (tpp) cc_final: 0.8197 (tpp) REVERT: V 108 ASP cc_start: 0.9328 (m-30) cc_final: 0.9018 (t0) REVERT: V 113 ASN cc_start: 0.8464 (t0) cc_final: 0.8093 (t0) REVERT: V 150 ILE cc_start: 0.8320 (tt) cc_final: 0.7760 (pt) REVERT: V 159 MET cc_start: 0.9128 (mmp) cc_final: 0.8506 (tmm) REVERT: W 21 ASN cc_start: 0.8252 (m110) cc_final: 0.7824 (m110) REVERT: W 25 GLN cc_start: 0.8430 (tp40) cc_final: 0.8111 (mt0) REVERT: W 61 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7952 (mm-40) REVERT: W 69 MET cc_start: 0.4726 (mtp) cc_final: 0.3955 (mmm) REVERT: W 97 TYR cc_start: 0.8483 (m-10) cc_final: 0.8110 (m-80) REVERT: W 163 ASN cc_start: 0.7534 (m-40) cc_final: 0.7093 (m-40) REVERT: X 88 MET cc_start: 0.9290 (ttm) cc_final: 0.9080 (ttt) REVERT: X 89 GLU cc_start: 0.8948 (tt0) cc_final: 0.8497 (tm-30) REVERT: X 109 ASP cc_start: 0.8768 (t70) cc_final: 0.8116 (m-30) REVERT: X 136 MET cc_start: 0.7800 (mmt) cc_final: 0.7539 (mmm) REVERT: X 166 PHE cc_start: 0.7838 (m-80) cc_final: 0.7555 (m-80) REVERT: Y 28 ARG cc_start: 0.9247 (ttp-170) cc_final: 0.8666 (ttm170) REVERT: Y 55 MET cc_start: 0.8938 (ttt) cc_final: 0.8728 (ttt) REVERT: Z 42 GLN cc_start: 0.9160 (tp40) cc_final: 0.8824 (tp40) REVERT: Z 59 GLU cc_start: 0.8931 (mp0) cc_final: 0.8326 (pm20) REVERT: Z 101 LYS cc_start: 0.9366 (tmtt) cc_final: 0.9032 (ttpp) REVERT: Z 119 ASP cc_start: 0.9513 (m-30) cc_final: 0.9058 (m-30) REVERT: Z 124 GLU cc_start: 0.9392 (tp30) cc_final: 0.9126 (tp30) REVERT: Z 187 MET cc_start: 0.8477 (ttt) cc_final: 0.8103 (mtp) REVERT: Z 196 THR cc_start: 0.9738 (p) cc_final: 0.9441 (t) REVERT: Z 233 GLU cc_start: 0.7401 (mp0) cc_final: 0.6941 (mp0) REVERT: Z 270 LYS cc_start: 0.9483 (tppt) cc_final: 0.9213 (tttp) REVERT: a 3 ILE cc_start: 0.7492 (mm) cc_final: 0.7198 (mm) REVERT: a 74 ASN cc_start: 0.9324 (t0) cc_final: 0.8945 (p0) REVERT: a 84 ARG cc_start: 0.8961 (ttm110) cc_final: 0.8569 (ttm-80) REVERT: a 98 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8564 (mt-10) REVERT: a 151 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8747 (mt0) REVERT: a 152 ASN cc_start: 0.9197 (m-40) cc_final: 0.8988 (t0) REVERT: a 165 TYR cc_start: 0.5748 (m-10) cc_final: 0.5486 (m-80) REVERT: a 167 ASP cc_start: 0.8401 (m-30) cc_final: 0.8146 (m-30) outliers start: 6 outliers final: 0 residues processed: 1649 average time/residue: 0.4599 time to fit residues: 1226.8198 Evaluate side-chains 1396 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1395 time to evaluate : 3.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 360 optimal weight: 0.0770 chunk 245 optimal weight: 5.9990 chunk 6 optimal weight: 0.2980 chunk 322 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 369 optimal weight: 3.9990 chunk 299 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 25 GLN ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN T 21 ASN T 78 ASN ** V 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 145 ASN ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 64 ASN Z 182 GLN ** Z 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 161 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36155 Z= 0.237 Angle : 0.719 43.057 49243 Z= 0.334 Chirality : 0.038 0.206 5448 Planarity : 0.004 0.055 6402 Dihedral : 10.887 89.934 6599 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.52 % Favored : 97.41 % Rotamer: Outliers : 0.09 % Allowed : 2.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.13), residues: 4448 helix: 1.42 (0.09), residues: 3311 sheet: 1.92 (0.77), residues: 28 loop : -0.83 (0.21), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 128 HIS 0.006 0.002 HIS G 140 PHE 0.025 0.002 PHE X 24 TYR 0.035 0.002 TYR Q 97 ARG 0.009 0.001 ARG K 33 *********************** 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 1628 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1625 time to evaluate : 4.004 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: A 18 PHE cc_start: 0.8172 (m-80) cc_final: 0.7671 (m-80) REVERT: A 38 MET cc_start: 0.9210 (mmt) cc_final: 0.8315 (tmm) REVERT: A 39 GLU cc_start: 0.9608 (tp30) cc_final: 0.9199 (mm-30) REVERT: A 49 GLN cc_start: 0.8848 (tp40) cc_final: 0.8355 (mm-40) REVERT: A 53 ASP cc_start: 0.8936 (t0) cc_final: 0.8604 (p0) REVERT: A 60 TYR cc_start: 0.9222 (m-80) cc_final: 0.8762 (m-80) REVERT: A 62 LYS cc_start: 0.9356 (tptt) cc_final: 0.8996 (tptt) REVERT: A 63 PHE cc_start: 0.9217 (m-80) cc_final: 0.8772 (m-80) REVERT: A 90 TYR cc_start: 0.9190 (m-10) cc_final: 0.8568 (m-80) REVERT: A 122 PHE cc_start: 0.9266 (m-80) cc_final: 0.9031 (m-80) REVERT: A 167 ASP cc_start: 0.9349 (t0) cc_final: 0.9013 (t0) REVERT: B 5 PHE cc_start: 0.8862 (m-80) cc_final: 0.8596 (m-80) REVERT: B 27 LEU cc_start: 0.9266 (mm) cc_final: 0.9060 (mm) REVERT: B 32 LYS cc_start: 0.9016 (ttpp) cc_final: 0.8705 (tppt) REVERT: B 59 LEU cc_start: 0.9072 (mm) cc_final: 0.8726 (tt) REVERT: B 89 GLU cc_start: 0.9396 (pt0) cc_final: 0.8917 (tt0) REVERT: B 120 GLN cc_start: 0.8754 (mt0) cc_final: 0.8006 (tm-30) REVERT: B 136 MET cc_start: 0.8602 (mtt) cc_final: 0.7498 (mtt) REVERT: B 145 ASN cc_start: 0.8751 (t0) cc_final: 0.8212 (p0) REVERT: B 159 MET cc_start: 0.9458 (mpp) cc_final: 0.9142 (mpp) REVERT: C 63 PHE cc_start: 0.9139 (m-10) cc_final: 0.8668 (m-10) REVERT: C 69 MET cc_start: 0.7682 (ttm) cc_final: 0.7253 (ttm) REVERT: C 94 MET cc_start: 0.9460 (mmt) cc_final: 0.9177 (mmm) REVERT: C 115 LEU cc_start: 0.8963 (pp) cc_final: 0.8567 (pp) REVERT: C 133 LEU cc_start: 0.9152 (mp) cc_final: 0.8859 (tp) REVERT: D 81 MET cc_start: 0.8028 (tpp) cc_final: 0.7391 (ttt) REVERT: D 88 MET cc_start: 0.8663 (mmm) cc_final: 0.8270 (mmm) REVERT: D 97 TYR cc_start: 0.9019 (m-10) cc_final: 0.8261 (m-80) REVERT: D 111 CYS cc_start: 0.8429 (t) cc_final: 0.8001 (t) REVERT: D 128 SER cc_start: 0.9466 (p) cc_final: 0.9245 (p) REVERT: D 146 ASP cc_start: 0.9420 (t0) cc_final: 0.9209 (t0) REVERT: D 154 ASP cc_start: 0.7846 (t0) cc_final: 0.7593 (t0) REVERT: E 25 GLN cc_start: 0.8944 (mt0) cc_final: 0.8631 (mt0) REVERT: E 38 MET cc_start: 0.8891 (mmt) cc_final: 0.8132 (tmm) REVERT: E 72 SER cc_start: 0.8897 (m) cc_final: 0.8327 (t) REVERT: E 109 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8563 (tt0) REVERT: E 121 THR cc_start: 0.9765 (p) cc_final: 0.9557 (t) REVERT: E 123 ASP cc_start: 0.8872 (m-30) cc_final: 0.8414 (t0) REVERT: E 167 ASP cc_start: 0.9434 (t0) cc_final: 0.8417 (t0) REVERT: E 171 ASN cc_start: 0.9214 (p0) cc_final: 0.8901 (p0) REVERT: F 1 MET cc_start: 0.8757 (tpp) cc_final: 0.8138 (tpp) REVERT: F 3 ASP cc_start: 0.9296 (p0) cc_final: 0.9073 (p0) REVERT: F 21 ASN cc_start: 0.8549 (m-40) cc_final: 0.7351 (t0) REVERT: F 35 ASN cc_start: 0.9400 (m-40) cc_final: 0.9057 (m-40) REVERT: F 76 TYR cc_start: 0.9002 (t80) cc_final: 0.8030 (t80) REVERT: F 88 MET cc_start: 0.9520 (tpp) cc_final: 0.9118 (tpp) REVERT: F 137 LYS cc_start: 0.9413 (ttpt) cc_final: 0.9198 (ttpt) REVERT: F 146 ASP cc_start: 0.8920 (t0) cc_final: 0.8603 (t0) REVERT: F 161 GLU cc_start: 0.9365 (mm-30) cc_final: 0.8734 (tp30) REVERT: G 5 ILE cc_start: 0.9212 (mp) cc_final: 0.8891 (tt) REVERT: G 28 ASP cc_start: 0.9050 (t0) cc_final: 0.8803 (t70) REVERT: G 30 ARG cc_start: 0.9350 (tmt-80) cc_final: 0.9133 (tmt-80) REVERT: G 33 ARG cc_start: 0.8973 (mtm110) cc_final: 0.8688 (mtm110) REVERT: G 46 ASN cc_start: 0.9400 (t0) cc_final: 0.9162 (t0) REVERT: G 74 TYR cc_start: 0.8990 (m-80) cc_final: 0.8748 (m-10) REVERT: G 79 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8719 (pp20) REVERT: G 97 TYR cc_start: 0.9404 (m-10) cc_final: 0.8970 (m-10) REVERT: G 123 ASP cc_start: 0.8865 (t0) cc_final: 0.8470 (t0) REVERT: G 124 LEU cc_start: 0.9206 (mt) cc_final: 0.8853 (mt) REVERT: G 163 ASN cc_start: 0.9442 (m-40) cc_final: 0.9091 (m-40) REVERT: H 1 MET cc_start: 0.8721 (mtt) cc_final: 0.8433 (mpp) REVERT: H 3 ASP cc_start: 0.9250 (p0) cc_final: 0.8859 (p0) REVERT: H 21 ASN cc_start: 0.8895 (m-40) cc_final: 0.8613 (t0) REVERT: H 117 GLU cc_start: 0.9300 (tp30) cc_final: 0.9072 (tp30) REVERT: H 145 ASN cc_start: 0.8314 (m-40) cc_final: 0.8114 (m-40) REVERT: I 47 ASN cc_start: 0.7934 (p0) cc_final: 0.7659 (p0) REVERT: I 51 LEU cc_start: 0.9270 (mt) cc_final: 0.8956 (mt) REVERT: I 60 TYR cc_start: 0.8244 (m-80) cc_final: 0.7977 (m-80) REVERT: I 110 TYR cc_start: 0.9199 (m-10) cc_final: 0.8880 (m-10) REVERT: I 119 ASN cc_start: 0.9404 (m110) cc_final: 0.9200 (m110) REVERT: I 127 SER cc_start: 0.9461 (p) cc_final: 0.9128 (t) REVERT: I 129 TYR cc_start: 0.8837 (m-10) cc_final: 0.8520 (m-10) REVERT: I 173 LEU cc_start: 0.9413 (tp) cc_final: 0.8817 (tt) REVERT: J 24 PHE cc_start: 0.7941 (m-80) cc_final: 0.7737 (m-80) REVERT: J 35 ASN cc_start: 0.9366 (m110) cc_final: 0.8564 (t0) REVERT: J 112 LEU cc_start: 0.9426 (mp) cc_final: 0.8933 (mm) REVERT: K 21 ASN cc_start: 0.8485 (p0) cc_final: 0.8201 (t0) REVERT: K 33 ARG cc_start: 0.8544 (ttm110) cc_final: 0.8172 (tpm170) REVERT: K 57 GLN cc_start: 0.8969 (pp30) cc_final: 0.8614 (mm-40) REVERT: K 97 TYR cc_start: 0.8615 (m-10) cc_final: 0.8060 (m-80) REVERT: L 7 LYS cc_start: 0.9320 (ttpp) cc_final: 0.9084 (ptmm) REVERT: L 33 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8963 (mp0) REVERT: L 41 VAL cc_start: 0.9551 (m) cc_final: 0.9256 (p) REVERT: L 63 GLN cc_start: 0.9421 (mt0) cc_final: 0.9002 (mt0) REVERT: L 80 ARG cc_start: 0.8997 (mtm-85) cc_final: 0.8698 (mtm-85) REVERT: L 88 MET cc_start: 0.8024 (mtm) cc_final: 0.7764 (ptm) REVERT: L 89 GLU cc_start: 0.9148 (pp20) cc_final: 0.8561 (tm-30) REVERT: L 90 ILE cc_start: 0.8944 (mt) cc_final: 0.8306 (mm) REVERT: L 103 ASP cc_start: 0.9417 (m-30) cc_final: 0.9133 (m-30) REVERT: L 113 ASN cc_start: 0.9458 (t0) cc_final: 0.8630 (t0) REVERT: L 146 ASP cc_start: 0.9252 (t0) cc_final: 0.8966 (t0) REVERT: L 159 MET cc_start: 0.9181 (mmt) cc_final: 0.8873 (mmt) REVERT: M 9 ILE cc_start: 0.9378 (tp) cc_final: 0.8853 (tp) REVERT: M 33 ARG cc_start: 0.9054 (tpt-90) cc_final: 0.8594 (ttt180) REVERT: M 81 LYS cc_start: 0.9032 (tmtt) cc_final: 0.8777 (mtpp) REVERT: M 94 MET cc_start: 0.9029 (mtt) cc_final: 0.8682 (mtt) REVERT: M 96 THR cc_start: 0.9453 (p) cc_final: 0.9213 (p) REVERT: M 99 LEU cc_start: 0.8973 (mt) cc_final: 0.8692 (tp) REVERT: M 107 MET cc_start: 0.8697 (mmm) cc_final: 0.8116 (mmm) REVERT: M 119 ASN cc_start: 0.9143 (p0) cc_final: 0.8831 (p0) REVERT: M 129 TYR cc_start: 0.8623 (m-80) cc_final: 0.8361 (m-80) REVERT: M 135 TYR cc_start: 0.9194 (t80) cc_final: 0.8894 (t80) REVERT: M 171 ASN cc_start: 0.8538 (p0) cc_final: 0.8253 (p0) REVERT: N 19 LEU cc_start: 0.8521 (mt) cc_final: 0.8289 (mt) REVERT: N 20 THR cc_start: 0.8435 (t) cc_final: 0.8093 (p) REVERT: N 35 ASN cc_start: 0.9528 (m-40) cc_final: 0.9045 (t0) REVERT: N 62 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8818 (tm-30) REVERT: N 65 GLN cc_start: 0.8456 (mp10) cc_final: 0.7885 (mp10) REVERT: N 80 ARG cc_start: 0.9119 (mtm-85) cc_final: 0.8227 (mtm-85) REVERT: N 87 ASP cc_start: 0.8896 (m-30) cc_final: 0.8351 (m-30) REVERT: N 88 MET cc_start: 0.8824 (ttp) cc_final: 0.7867 (tpp) REVERT: N 97 TYR cc_start: 0.9072 (m-10) cc_final: 0.8549 (m-80) REVERT: N 136 MET cc_start: 0.8900 (mtm) cc_final: 0.8654 (mtm) REVERT: O 15 GLN cc_start: 0.9164 (mt0) cc_final: 0.8920 (mp10) REVERT: O 19 LEU cc_start: 0.8407 (mm) cc_final: 0.8151 (mm) REVERT: O 21 ASN cc_start: 0.7926 (t0) cc_final: 0.7507 (t0) REVERT: O 23 GLU cc_start: 0.9648 (mp0) cc_final: 0.9422 (mp0) REVERT: O 60 TYR cc_start: 0.8190 (m-10) cc_final: 0.7934 (m-10) REVERT: O 104 THR cc_start: 0.9143 (p) cc_final: 0.8757 (p) REVERT: O 111 LEU cc_start: 0.9311 (tp) cc_final: 0.9080 (tp) REVERT: O 129 TYR cc_start: 0.9037 (m-80) cc_final: 0.8401 (m-80) REVERT: O 131 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8905 (pt0) REVERT: P 9 VAL cc_start: 0.9773 (t) cc_final: 0.9418 (p) REVERT: P 23 GLN cc_start: 0.8584 (mt0) cc_final: 0.8379 (mt0) REVERT: P 97 TYR cc_start: 0.9027 (m-10) cc_final: 0.8509 (m-10) REVERT: P 104 SER cc_start: 0.9112 (p) cc_final: 0.8794 (p) REVERT: P 113 ASN cc_start: 0.8664 (t0) cc_final: 0.8407 (t0) REVERT: P 122 LEU cc_start: 0.8813 (mm) cc_final: 0.8576 (mm) REVERT: P 124 THR cc_start: 0.9082 (m) cc_final: 0.8795 (p) REVERT: P 159 MET cc_start: 0.9012 (mmm) cc_final: 0.8644 (mmm) REVERT: Q 2 LYS cc_start: 0.8649 (mttm) cc_final: 0.8216 (mmtm) REVERT: Q 25 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8615 (mm-40) REVERT: Q 39 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7290 (pt0) REVERT: Q 62 LYS cc_start: 0.7180 (ttmm) cc_final: 0.6756 (ttmt) REVERT: Q 63 PHE cc_start: 0.7976 (m-10) cc_final: 0.7698 (m-10) REVERT: Q 69 MET cc_start: 0.6416 (ptm) cc_final: 0.5981 (ptm) REVERT: Q 94 MET cc_start: 0.6237 (tpp) cc_final: 0.4855 (mmm) REVERT: Q 108 ASP cc_start: 0.9245 (m-30) cc_final: 0.8993 (m-30) REVERT: R 29 ASN cc_start: 0.8055 (t0) cc_final: 0.7417 (m110) REVERT: R 38 LEU cc_start: 0.8653 (mt) cc_final: 0.8212 (mp) REVERT: R 87 ASP cc_start: 0.8073 (m-30) cc_final: 0.7816 (m-30) REVERT: R 88 MET cc_start: 0.9550 (mmm) cc_final: 0.9229 (mtm) REVERT: R 111 CYS cc_start: 0.8649 (t) cc_final: 0.8249 (t) REVERT: R 128 SER cc_start: 0.8464 (m) cc_final: 0.8158 (m) REVERT: R 136 MET cc_start: 0.8790 (ttp) cc_final: 0.8203 (tmm) REVERT: R 159 MET cc_start: 0.8539 (mmp) cc_final: 0.7788 (ptt) REVERT: S 44 LEU cc_start: 0.9714 (mt) cc_final: 0.9148 (tp) REVERT: S 49 GLN cc_start: 0.9387 (tp-100) cc_final: 0.8736 (pm20) REVERT: S 73 GLN cc_start: 0.8916 (pt0) cc_final: 0.8467 (pm20) REVERT: S 74 TYR cc_start: 0.9201 (m-80) cc_final: 0.8675 (m-80) REVERT: S 79 GLU cc_start: 0.8291 (mp0) cc_final: 0.8088 (tm-30) REVERT: S 84 CYS cc_start: 0.9098 (t) cc_final: 0.8789 (t) REVERT: S 97 TYR cc_start: 0.9418 (m-80) cc_final: 0.8822 (m-80) REVERT: S 137 LYS cc_start: 0.9268 (ttpt) cc_final: 0.8921 (tptt) REVERT: S 139 ASN cc_start: 0.9158 (m110) cc_final: 0.8774 (m110) REVERT: T 1 MET cc_start: 0.7941 (ttm) cc_final: 0.7035 (tmm) REVERT: T 9 VAL cc_start: 0.9208 (t) cc_final: 0.8925 (p) REVERT: T 13 ASP cc_start: 0.8685 (t0) cc_final: 0.8358 (t0) REVERT: T 15 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7422 (mmp80) REVERT: T 19 LEU cc_start: 0.8226 (mt) cc_final: 0.7607 (mp) REVERT: T 23 GLN cc_start: 0.8266 (mt0) cc_final: 0.7805 (mp10) REVERT: T 47 ASN cc_start: 0.7867 (t0) cc_final: 0.7323 (t0) REVERT: T 63 GLN cc_start: 0.7157 (mm-40) cc_final: 0.6679 (tp-100) REVERT: T 93 ARG cc_start: 0.8536 (ttp-170) cc_final: 0.6924 (tpp80) REVERT: U 28 ASP cc_start: 0.9156 (t70) cc_final: 0.8899 (t0) REVERT: U 65 TYR cc_start: 0.9257 (p90) cc_final: 0.8937 (p90) REVERT: U 109 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8649 (tm-30) REVERT: U 123 ASP cc_start: 0.9472 (t0) cc_final: 0.9259 (t0) REVERT: V 11 GLN cc_start: 0.8898 (tt0) cc_final: 0.8361 (tp40) REVERT: V 60 PHE cc_start: 0.9113 (m-80) cc_final: 0.8843 (m-80) REVERT: V 62 GLU cc_start: 0.9425 (tm-30) cc_final: 0.9171 (tm-30) REVERT: V 67 ILE cc_start: 0.8983 (pt) cc_final: 0.8780 (mt) REVERT: V 68 GLN cc_start: 0.9032 (pt0) cc_final: 0.8805 (pt0) REVERT: V 81 MET cc_start: 0.8622 (tpp) cc_final: 0.8153 (tpp) REVERT: V 150 ILE cc_start: 0.8590 (tt) cc_final: 0.7975 (pt) REVERT: V 159 MET cc_start: 0.9232 (mmp) cc_final: 0.8617 (tmm) REVERT: W 1 MET cc_start: 0.5419 (pmm) cc_final: 0.4717 (pmm) REVERT: W 3 THR cc_start: 0.7849 (m) cc_final: 0.7583 (m) REVERT: W 21 ASN cc_start: 0.8318 (m110) cc_final: 0.7810 (m110) REVERT: W 24 LEU cc_start: 0.9200 (mt) cc_final: 0.8954 (mt) REVERT: W 25 GLN cc_start: 0.8139 (tp40) cc_final: 0.7905 (mt0) REVERT: W 61 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7925 (mm-40) REVERT: W 69 MET cc_start: 0.5313 (mtp) cc_final: 0.4561 (mmm) REVERT: W 97 TYR cc_start: 0.8442 (m-10) cc_final: 0.7919 (m-80) REVERT: X 88 MET cc_start: 0.9286 (ttm) cc_final: 0.9054 (ttt) REVERT: X 89 GLU cc_start: 0.9396 (tt0) cc_final: 0.8972 (tm-30) REVERT: X 90 ILE cc_start: 0.9075 (tt) cc_final: 0.8821 (tt) REVERT: X 166 PHE cc_start: 0.7842 (m-80) cc_final: 0.7588 (m-80) REVERT: Y 20 PHE cc_start: 0.8739 (m-10) cc_final: 0.8396 (m-10) REVERT: Z 36 ILE cc_start: 0.9161 (mt) cc_final: 0.8887 (tp) REVERT: Z 42 GLN cc_start: 0.9261 (tp40) cc_final: 0.8951 (tp40) REVERT: Z 101 LYS cc_start: 0.9378 (tmtt) cc_final: 0.9119 (ttpp) REVERT: Z 110 ASP cc_start: 0.8964 (t70) cc_final: 0.8753 (m-30) REVERT: Z 119 ASP cc_start: 0.9534 (m-30) cc_final: 0.9074 (m-30) REVERT: Z 124 GLU cc_start: 0.9387 (tp30) cc_final: 0.9125 (tp30) REVERT: Z 187 MET cc_start: 0.8384 (ttt) cc_final: 0.7968 (mtp) REVERT: Z 196 THR cc_start: 0.9717 (p) cc_final: 0.9417 (t) REVERT: Z 233 GLU cc_start: 0.7339 (mp0) cc_final: 0.6923 (mp0) REVERT: Z 270 LYS cc_start: 0.9487 (tppt) cc_final: 0.9221 (tttp) REVERT: a 74 ASN cc_start: 0.9352 (t0) cc_final: 0.8849 (p0) REVERT: a 84 ARG cc_start: 0.8928 (ttm110) cc_final: 0.8335 (ttm-80) REVERT: a 98 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8494 (mt-10) REVERT: a 152 ASN cc_start: 0.9341 (m-40) cc_final: 0.8839 (t0) outliers start: 3 outliers final: 0 residues processed: 1627 average time/residue: 0.4686 time to fit residues: 1228.9494 Evaluate side-chains 1347 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1347 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 145 optimal weight: 0.7980 chunk 389 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 254 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 433 optimal weight: 7.9990 chunk 359 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 63 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 147 GLN F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 ASN ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 ASN ** X 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 64 ASN ** Z 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 161 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 36155 Z= 0.200 Angle : 0.712 42.909 49243 Z= 0.327 Chirality : 0.038 0.189 5448 Planarity : 0.004 0.055 6402 Dihedral : 10.817 89.906 6599 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.38 % Favored : 97.53 % Rotamer: Outliers : 0.06 % Allowed : 2.06 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.13), residues: 4448 helix: 1.44 (0.09), residues: 3303 sheet: 1.76 (0.74), residues: 28 loop : -0.78 (0.21), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 128 HIS 0.007 0.002 HIS Z 117 PHE 0.051 0.002 PHE T 166 TYR 0.046 0.002 TYR M 97 ARG 0.006 0.001 ARG Y 64 *********************** 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 1675 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1673 time to evaluate : 3.795 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: A 18 PHE cc_start: 0.8150 (m-80) cc_final: 0.7635 (m-80) REVERT: A 38 MET cc_start: 0.9214 (mmt) cc_final: 0.8448 (tmm) REVERT: A 39 GLU cc_start: 0.9534 (tp30) cc_final: 0.8926 (mm-30) REVERT: A 46 ASN cc_start: 0.9304 (m-40) cc_final: 0.8973 (m110) REVERT: A 49 GLN cc_start: 0.8819 (tp40) cc_final: 0.8370 (mm-40) REVERT: A 53 ASP cc_start: 0.9087 (t0) cc_final: 0.8632 (p0) REVERT: A 60 TYR cc_start: 0.9263 (m-80) cc_final: 0.8737 (m-80) REVERT: A 62 LYS cc_start: 0.9373 (tptt) cc_final: 0.9025 (tptt) REVERT: A 63 PHE cc_start: 0.9271 (m-80) cc_final: 0.8816 (m-80) REVERT: A 90 TYR cc_start: 0.9176 (m-10) cc_final: 0.8583 (m-80) REVERT: A 98 CYS cc_start: 0.9548 (t) cc_final: 0.9274 (t) REVERT: A 167 ASP cc_start: 0.9396 (t0) cc_final: 0.9033 (t0) REVERT: B 32 LYS cc_start: 0.9000 (ttpp) cc_final: 0.8531 (tppt) REVERT: B 36 LYS cc_start: 0.9066 (mtmm) cc_final: 0.8819 (mppt) REVERT: B 78 ASN cc_start: 0.8395 (t0) cc_final: 0.7984 (t0) REVERT: B 89 GLU cc_start: 0.9373 (pt0) cc_final: 0.8911 (tt0) REVERT: B 103 ASP cc_start: 0.9029 (t0) cc_final: 0.8787 (t70) REVERT: B 108 ASP cc_start: 0.9377 (m-30) cc_final: 0.8969 (m-30) REVERT: B 112 LEU cc_start: 0.9301 (mt) cc_final: 0.8821 (mp) REVERT: B 120 GLN cc_start: 0.8671 (mt0) cc_final: 0.7937 (tm-30) REVERT: B 136 MET cc_start: 0.8712 (mtt) cc_final: 0.7365 (mtt) REVERT: B 145 ASN cc_start: 0.8708 (t0) cc_final: 0.8194 (p0) REVERT: B 159 MET cc_start: 0.9451 (mpp) cc_final: 0.9092 (mpp) REVERT: C 69 MET cc_start: 0.7648 (ttm) cc_final: 0.7292 (ttm) REVERT: C 94 MET cc_start: 0.9551 (mmt) cc_final: 0.9206 (mmm) REVERT: C 115 LEU cc_start: 0.8883 (pp) cc_final: 0.8614 (pp) REVERT: C 119 ASN cc_start: 0.8552 (m110) cc_final: 0.8082 (p0) REVERT: D 88 MET cc_start: 0.8687 (mmm) cc_final: 0.8263 (mmm) REVERT: D 97 TYR cc_start: 0.8862 (m-10) cc_final: 0.8247 (m-80) REVERT: D 111 CYS cc_start: 0.8724 (t) cc_final: 0.8338 (t) REVERT: D 127 SER cc_start: 0.9246 (p) cc_final: 0.8971 (t) REVERT: D 128 SER cc_start: 0.9463 (p) cc_final: 0.9031 (p) REVERT: D 146 ASP cc_start: 0.9434 (t0) cc_final: 0.9135 (t0) REVERT: D 154 ASP cc_start: 0.7855 (t0) cc_final: 0.7583 (t0) REVERT: E 25 GLN cc_start: 0.8957 (mt0) cc_final: 0.8554 (mt0) REVERT: E 38 MET cc_start: 0.8901 (mmt) cc_final: 0.8100 (tmm) REVERT: E 60 TYR cc_start: 0.9443 (m-10) cc_final: 0.8995 (m-10) REVERT: E 72 SER cc_start: 0.8803 (m) cc_final: 0.8201 (t) REVERT: E 83 LYS cc_start: 0.9395 (tppp) cc_final: 0.9073 (tppp) REVERT: E 86 ARG cc_start: 0.8663 (ttp80) cc_final: 0.7578 (ttp80) REVERT: E 109 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8521 (tt0) REVERT: E 123 ASP cc_start: 0.8913 (m-30) cc_final: 0.8431 (t0) REVERT: E 167 ASP cc_start: 0.9401 (t0) cc_final: 0.8299 (t0) REVERT: E 171 ASN cc_start: 0.9172 (p0) cc_final: 0.8906 (p0) REVERT: F 1 MET cc_start: 0.8702 (tpp) cc_final: 0.8120 (tpp) REVERT: F 3 ASP cc_start: 0.9226 (p0) cc_final: 0.8938 (p0) REVERT: F 21 ASN cc_start: 0.8730 (m-40) cc_final: 0.7578 (t0) REVERT: F 25 ASP cc_start: 0.8818 (m-30) cc_final: 0.7991 (m-30) REVERT: F 29 ASN cc_start: 0.9648 (m-40) cc_final: 0.9342 (m-40) REVERT: F 35 ASN cc_start: 0.9380 (m-40) cc_final: 0.9058 (m-40) REVERT: F 76 TYR cc_start: 0.8703 (t80) cc_final: 0.8045 (t80) REVERT: F 137 LYS cc_start: 0.9350 (ttpt) cc_final: 0.9057 (ttpt) REVERT: F 146 ASP cc_start: 0.8980 (t0) cc_final: 0.8612 (t0) REVERT: F 161 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8747 (tp30) REVERT: F 165 TYR cc_start: 0.9489 (m-80) cc_final: 0.9147 (m-80) REVERT: G 5 ILE cc_start: 0.9198 (mp) cc_final: 0.8961 (tt) REVERT: G 25 GLN cc_start: 0.9371 (mt0) cc_final: 0.9088 (mt0) REVERT: G 28 ASP cc_start: 0.8991 (t0) cc_final: 0.8697 (t70) REVERT: G 46 ASN cc_start: 0.9410 (t0) cc_final: 0.9166 (t0) REVERT: G 74 TYR cc_start: 0.8949 (m-80) cc_final: 0.8683 (m-10) REVERT: G 79 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8720 (pp20) REVERT: G 97 TYR cc_start: 0.9406 (m-10) cc_final: 0.9011 (m-10) REVERT: G 99 LEU cc_start: 0.9114 (tp) cc_final: 0.8614 (tp) REVERT: G 123 ASP cc_start: 0.8959 (t0) cc_final: 0.8578 (t0) REVERT: G 124 LEU cc_start: 0.9217 (mt) cc_final: 0.8704 (mp) REVERT: G 163 ASN cc_start: 0.9465 (m-40) cc_final: 0.9053 (m-40) REVERT: H 1 MET cc_start: 0.8928 (mtt) cc_final: 0.8318 (mpp) REVERT: H 3 ASP cc_start: 0.9247 (p0) cc_final: 0.8823 (p0) REVERT: H 21 ASN cc_start: 0.8869 (m-40) cc_final: 0.8613 (t0) REVERT: H 91 ILE cc_start: 0.9494 (mm) cc_final: 0.9166 (tp) REVERT: H 117 GLU cc_start: 0.9377 (tp30) cc_final: 0.9060 (tp30) REVERT: H 145 ASN cc_start: 0.8319 (m-40) cc_final: 0.7808 (m-40) REVERT: I 9 ILE cc_start: 0.9728 (tp) cc_final: 0.9508 (tp) REVERT: I 37 SER cc_start: 0.9124 (p) cc_final: 0.8878 (p) REVERT: I 47 ASN cc_start: 0.7994 (p0) cc_final: 0.7767 (p0) REVERT: I 51 LEU cc_start: 0.9211 (mt) cc_final: 0.8925 (mt) REVERT: I 60 TYR cc_start: 0.8269 (m-80) cc_final: 0.7874 (m-80) REVERT: I 115 LEU cc_start: 0.9070 (tp) cc_final: 0.8693 (tp) REVERT: I 127 SER cc_start: 0.9423 (p) cc_final: 0.8993 (t) REVERT: I 129 TYR cc_start: 0.8829 (m-10) cc_final: 0.8505 (m-10) REVERT: I 167 ASP cc_start: 0.9447 (m-30) cc_final: 0.9234 (m-30) REVERT: I 173 LEU cc_start: 0.9409 (tp) cc_final: 0.8840 (tt) REVERT: J 24 PHE cc_start: 0.7966 (m-80) cc_final: 0.7736 (m-80) REVERT: J 35 ASN cc_start: 0.9359 (m110) cc_final: 0.8415 (t0) REVERT: J 112 LEU cc_start: 0.9405 (mp) cc_final: 0.8905 (mm) REVERT: J 159 MET cc_start: 0.8958 (mmp) cc_final: 0.8544 (mmm) REVERT: K 21 ASN cc_start: 0.8366 (p0) cc_final: 0.7965 (t0) REVERT: K 33 ARG cc_start: 0.8542 (ttm110) cc_final: 0.8156 (tpm170) REVERT: K 57 GLN cc_start: 0.8947 (pp30) cc_final: 0.8612 (mm-40) REVERT: K 133 LEU cc_start: 0.9030 (mt) cc_final: 0.8240 (tt) REVERT: K 139 ASN cc_start: 0.9255 (m-40) cc_final: 0.8620 (t0) REVERT: K 166 ILE cc_start: 0.9387 (mm) cc_final: 0.9024 (mm) REVERT: L 7 LYS cc_start: 0.9294 (ttpp) cc_final: 0.8889 (ptmm) REVERT: L 63 GLN cc_start: 0.9383 (mt0) cc_final: 0.9111 (mt0) REVERT: L 80 ARG cc_start: 0.8895 (mtm-85) cc_final: 0.8641 (mtt-85) REVERT: L 89 GLU cc_start: 0.9090 (pp20) cc_final: 0.8502 (tm-30) REVERT: L 90 ILE cc_start: 0.8866 (mt) cc_final: 0.8152 (mm) REVERT: L 113 ASN cc_start: 0.9315 (t0) cc_final: 0.8501 (t0) REVERT: L 118 THR cc_start: 0.9688 (p) cc_final: 0.9417 (p) REVERT: L 137 LYS cc_start: 0.9123 (tttt) cc_final: 0.8641 (ttmt) REVERT: L 146 ASP cc_start: 0.9204 (t0) cc_final: 0.8897 (t0) REVERT: L 159 MET cc_start: 0.9123 (mmt) cc_final: 0.8806 (mmt) REVERT: L 161 GLU cc_start: 0.9161 (tt0) cc_final: 0.8691 (tp30) REVERT: M 9 ILE cc_start: 0.9357 (tp) cc_final: 0.8801 (tp) REVERT: M 15 GLN cc_start: 0.9480 (mt0) cc_final: 0.9278 (mt0) REVERT: M 53 ASP cc_start: 0.9415 (t0) cc_final: 0.9107 (t0) REVERT: M 57 GLN cc_start: 0.9600 (mm-40) cc_final: 0.9108 (mm-40) REVERT: M 81 LYS cc_start: 0.8978 (tmtt) cc_final: 0.8721 (mtpp) REVERT: M 99 LEU cc_start: 0.9070 (mt) cc_final: 0.8783 (tp) REVERT: M 107 MET cc_start: 0.8708 (mmm) cc_final: 0.8087 (mmm) REVERT: M 115 LEU cc_start: 0.9121 (tt) cc_final: 0.8911 (tp) REVERT: M 129 TYR cc_start: 0.8431 (m-80) cc_final: 0.8172 (m-80) REVERT: M 171 ASN cc_start: 0.8385 (p0) cc_final: 0.8122 (p0) REVERT: N 20 THR cc_start: 0.8443 (t) cc_final: 0.8174 (p) REVERT: N 35 ASN cc_start: 0.9524 (m-40) cc_final: 0.9010 (t0) REVERT: N 87 ASP cc_start: 0.8902 (m-30) cc_final: 0.8612 (m-30) REVERT: N 88 MET cc_start: 0.8777 (ttp) cc_final: 0.7769 (mtp) REVERT: N 97 TYR cc_start: 0.9096 (m-10) cc_final: 0.8473 (m-80) REVERT: N 111 CYS cc_start: 0.9758 (t) cc_final: 0.9515 (t) REVERT: N 119 TYR cc_start: 0.9358 (m-10) cc_final: 0.8770 (m-10) REVERT: N 135 LYS cc_start: 0.8458 (mmmm) cc_final: 0.8183 (mmmm) REVERT: N 159 MET cc_start: 0.8876 (tpp) cc_final: 0.8383 (tpt) REVERT: O 15 GLN cc_start: 0.9119 (mt0) cc_final: 0.8889 (mp10) REVERT: O 19 LEU cc_start: 0.8692 (mm) cc_final: 0.8274 (mm) REVERT: O 60 TYR cc_start: 0.8369 (m-10) cc_final: 0.8096 (m-10) REVERT: O 68 THR cc_start: 0.7772 (t) cc_final: 0.7548 (m) REVERT: O 94 MET cc_start: 0.9579 (mmp) cc_final: 0.9328 (mmp) REVERT: O 104 THR cc_start: 0.9148 (p) cc_final: 0.8723 (p) REVERT: O 111 LEU cc_start: 0.9290 (tp) cc_final: 0.8989 (tp) REVERT: O 129 TYR cc_start: 0.9019 (m-80) cc_final: 0.8366 (m-80) REVERT: O 131 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8904 (pt0) REVERT: O 170 ILE cc_start: 0.9116 (tt) cc_final: 0.8904 (tp) REVERT: P 9 VAL cc_start: 0.9777 (t) cc_final: 0.9365 (p) REVERT: P 97 TYR cc_start: 0.8952 (m-10) cc_final: 0.8335 (m-80) REVERT: P 104 SER cc_start: 0.9249 (p) cc_final: 0.8966 (p) REVERT: P 113 ASN cc_start: 0.8645 (t0) cc_final: 0.8300 (t0) REVERT: P 159 MET cc_start: 0.9096 (mmm) cc_final: 0.8889 (mmm) REVERT: Q 1 MET cc_start: 0.7103 (mmm) cc_final: 0.6284 (mmm) REVERT: Q 25 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8736 (mm-40) REVERT: Q 39 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7185 (mt-10) REVERT: Q 62 LYS cc_start: 0.6927 (ttmm) cc_final: 0.6706 (ttmm) REVERT: Q 69 MET cc_start: 0.6840 (ptm) cc_final: 0.6431 (ptm) REVERT: Q 94 MET cc_start: 0.6401 (tpp) cc_final: 0.4943 (mmm) REVERT: Q 108 ASP cc_start: 0.9315 (m-30) cc_final: 0.9008 (m-30) REVERT: R 25 ASP cc_start: 0.6587 (m-30) cc_final: 0.6268 (m-30) REVERT: R 29 ASN cc_start: 0.8072 (t0) cc_final: 0.7421 (m110) REVERT: R 30 LEU cc_start: 0.5995 (mm) cc_final: 0.5716 (mm) REVERT: R 38 LEU cc_start: 0.8672 (mt) cc_final: 0.8228 (mp) REVERT: R 87 ASP cc_start: 0.8053 (m-30) cc_final: 0.7627 (m-30) REVERT: R 88 MET cc_start: 0.9542 (mmm) cc_final: 0.9203 (mtm) REVERT: R 111 CYS cc_start: 0.8621 (t) cc_final: 0.8205 (t) REVERT: R 128 SER cc_start: 0.8387 (m) cc_final: 0.8092 (m) REVERT: R 136 MET cc_start: 0.8968 (ttp) cc_final: 0.8029 (tmm) REVERT: R 159 MET cc_start: 0.8523 (mmp) cc_final: 0.7734 (ptt) REVERT: S 44 LEU cc_start: 0.9711 (mt) cc_final: 0.9346 (tp) REVERT: S 49 GLN cc_start: 0.9436 (tp-100) cc_final: 0.8820 (pm20) REVERT: S 73 GLN cc_start: 0.9048 (pt0) cc_final: 0.8625 (pm20) REVERT: S 74 TYR cc_start: 0.9160 (m-80) cc_final: 0.8716 (m-80) REVERT: S 79 GLU cc_start: 0.8420 (mp0) cc_final: 0.8054 (tm-30) REVERT: S 84 CYS cc_start: 0.8995 (t) cc_final: 0.8718 (t) REVERT: S 90 TYR cc_start: 0.9184 (m-10) cc_final: 0.8845 (m-10) REVERT: S 97 TYR cc_start: 0.9423 (m-80) cc_final: 0.8846 (m-80) REVERT: S 139 ASN cc_start: 0.8913 (m110) cc_final: 0.8527 (m110) REVERT: T 9 VAL cc_start: 0.9183 (t) cc_final: 0.8912 (p) REVERT: T 13 ASP cc_start: 0.8649 (t0) cc_final: 0.8374 (t0) REVERT: T 15 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7305 (mmm160) REVERT: T 47 ASN cc_start: 0.7888 (t0) cc_final: 0.7080 (t0) REVERT: T 63 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7237 (tp-100) REVERT: U 28 ASP cc_start: 0.9157 (t70) cc_final: 0.8952 (t0) REVERT: U 65 TYR cc_start: 0.9264 (p90) cc_final: 0.8954 (p90) REVERT: U 109 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8528 (tm-30) REVERT: U 117 GLU cc_start: 0.9329 (pt0) cc_final: 0.9061 (mp0) REVERT: U 123 ASP cc_start: 0.9445 (t0) cc_final: 0.9189 (t0) REVERT: V 11 GLN cc_start: 0.8933 (tt0) cc_final: 0.8372 (tp40) REVERT: V 17 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8093 (mp0) REVERT: V 33 GLU cc_start: 0.9055 (mp0) cc_final: 0.8642 (mp0) REVERT: V 60 PHE cc_start: 0.9134 (m-80) cc_final: 0.8904 (m-80) REVERT: V 62 GLU cc_start: 0.9455 (tm-30) cc_final: 0.9227 (tm-30) REVERT: V 67 ILE cc_start: 0.8960 (pt) cc_final: 0.8703 (mt) REVERT: V 68 GLN cc_start: 0.9013 (pt0) cc_final: 0.8649 (pt0) REVERT: V 150 ILE cc_start: 0.8567 (tt) cc_final: 0.7938 (pt) REVERT: V 159 MET cc_start: 0.9281 (mmp) cc_final: 0.8621 (tmm) REVERT: W 3 THR cc_start: 0.7800 (m) cc_final: 0.7586 (m) REVERT: W 24 LEU cc_start: 0.9173 (mt) cc_final: 0.8936 (mt) REVERT: W 61 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7963 (mm-40) REVERT: W 69 MET cc_start: 0.5274 (mtp) cc_final: 0.4535 (mmm) REVERT: W 94 MET cc_start: 0.8901 (ppp) cc_final: 0.8342 (ppp) REVERT: W 97 TYR cc_start: 0.8222 (m-10) cc_final: 0.7763 (m-80) REVERT: W 111 LEU cc_start: 0.8296 (pt) cc_final: 0.7752 (pp) REVERT: W 163 ASN cc_start: 0.7415 (m-40) cc_final: 0.7210 (m-40) REVERT: X 52 VAL cc_start: 0.9158 (t) cc_final: 0.8916 (p) REVERT: X 88 MET cc_start: 0.9222 (ttm) cc_final: 0.8893 (ttt) REVERT: X 89 GLU cc_start: 0.9336 (tt0) cc_final: 0.8904 (tm-30) REVERT: X 90 ILE cc_start: 0.9106 (tt) cc_final: 0.8828 (tt) REVERT: Y 20 PHE cc_start: 0.8706 (m-10) cc_final: 0.8361 (m-10) REVERT: Y 36 MET cc_start: 0.8950 (mmp) cc_final: 0.8718 (mmp) REVERT: Y 55 MET cc_start: 0.8781 (ttt) cc_final: 0.8552 (ttt) REVERT: Z 36 ILE cc_start: 0.9075 (mt) cc_final: 0.8797 (pt) REVERT: Z 42 GLN cc_start: 0.9335 (tp40) cc_final: 0.8963 (tp40) REVERT: Z 101 LYS cc_start: 0.9298 (tmtt) cc_final: 0.9019 (ttpp) REVERT: Z 110 ASP cc_start: 0.9025 (t70) cc_final: 0.8774 (m-30) REVERT: Z 119 ASP cc_start: 0.9524 (m-30) cc_final: 0.8766 (m-30) REVERT: Z 124 GLU cc_start: 0.9348 (tp30) cc_final: 0.9106 (tp30) REVERT: Z 129 ASP cc_start: 0.9034 (t0) cc_final: 0.8713 (t0) REVERT: Z 134 ILE cc_start: 0.9313 (mm) cc_final: 0.9051 (mm) REVERT: Z 187 MET cc_start: 0.8363 (ttt) cc_final: 0.8008 (mtt) REVERT: Z 196 THR cc_start: 0.9706 (p) cc_final: 0.9397 (t) REVERT: Z 233 GLU cc_start: 0.7038 (mp0) cc_final: 0.6750 (mp0) REVERT: Z 270 LYS cc_start: 0.9476 (tppt) cc_final: 0.9200 (tttp) REVERT: a 74 ASN cc_start: 0.9303 (t0) cc_final: 0.8826 (p0) REVERT: a 84 ARG cc_start: 0.8964 (ttm110) cc_final: 0.8623 (ttm-80) REVERT: a 98 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8423 (mt-10) REVERT: a 152 ASN cc_start: 0.9074 (m-40) cc_final: 0.8832 (t0) outliers start: 2 outliers final: 0 residues processed: 1675 average time/residue: 0.4565 time to fit residues: 1234.7779 Evaluate side-chains 1388 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1388 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 417 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 246 optimal weight: 8.9990 chunk 316 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 364 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 431 optimal weight: 6.9990 chunk 270 optimal weight: 0.4980 chunk 263 optimal weight: 0.9980 chunk 199 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 47 ASN S 163 ASN U 139 ASN ** V 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 141 ASN ** Z 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 161 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 36155 Z= 0.293 Angle : 0.763 43.069 49243 Z= 0.361 Chirality : 0.040 0.196 5448 Planarity : 0.004 0.055 6402 Dihedral : 10.974 89.007 6599 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.17 % Rotamer: Outliers : 0.03 % Allowed : 1.59 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.13), residues: 4448 helix: 1.28 (0.09), residues: 3265 sheet: 1.66 (0.72), residues: 28 loop : -0.92 (0.20), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP U 128 HIS 0.007 0.002 HIS E 140 PHE 0.027 0.002 PHE B 60 TYR 0.060 0.002 TYR R 97 ARG 0.013 0.001 ARG T 86 *********************** 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 1573 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1572 time to evaluate : 3.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8193 (m-80) cc_final: 0.7629 (m-10) REVERT: A 49 GLN cc_start: 0.8861 (tp40) cc_final: 0.8405 (mm-40) REVERT: A 53 ASP cc_start: 0.8998 (t0) cc_final: 0.8480 (p0) REVERT: A 62 LYS cc_start: 0.9326 (tptt) cc_final: 0.8986 (tptt) REVERT: A 63 PHE cc_start: 0.9325 (m-80) cc_final: 0.8801 (m-80) REVERT: A 90 TYR cc_start: 0.9136 (m-10) cc_final: 0.8763 (m-80) REVERT: A 98 CYS cc_start: 0.9563 (t) cc_final: 0.9170 (m) REVERT: A 167 ASP cc_start: 0.9456 (t0) cc_final: 0.9112 (t0) REVERT: B 32 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8651 (tppt) REVERT: B 36 LYS cc_start: 0.9239 (mtmm) cc_final: 0.8927 (mppt) REVERT: B 89 GLU cc_start: 0.9435 (pt0) cc_final: 0.9021 (tt0) REVERT: B 108 ASP cc_start: 0.9356 (m-30) cc_final: 0.8894 (m-30) REVERT: B 112 LEU cc_start: 0.9385 (mt) cc_final: 0.8889 (mp) REVERT: B 120 GLN cc_start: 0.8783 (mt0) cc_final: 0.8002 (tm-30) REVERT: B 136 MET cc_start: 0.8846 (mtt) cc_final: 0.7679 (mtt) REVERT: B 145 ASN cc_start: 0.8790 (t0) cc_final: 0.8385 (p0) REVERT: C 69 MET cc_start: 0.7861 (ttm) cc_final: 0.7162 (ttm) REVERT: C 94 MET cc_start: 0.9535 (mmt) cc_final: 0.9197 (mmm) REVERT: C 115 LEU cc_start: 0.8901 (pp) cc_final: 0.8620 (pp) REVERT: C 118 ILE cc_start: 0.9304 (tp) cc_final: 0.9066 (tp) REVERT: C 119 ASN cc_start: 0.8665 (m110) cc_final: 0.8109 (p0) REVERT: D 49 SER cc_start: 0.8997 (p) cc_final: 0.8794 (p) REVERT: D 97 TYR cc_start: 0.9028 (m-10) cc_final: 0.8302 (m-80) REVERT: D 111 CYS cc_start: 0.8772 (t) cc_final: 0.8407 (t) REVERT: D 127 SER cc_start: 0.9288 (p) cc_final: 0.9056 (t) REVERT: D 128 SER cc_start: 0.9493 (p) cc_final: 0.9090 (p) REVERT: D 146 ASP cc_start: 0.9473 (t0) cc_final: 0.9253 (t0) REVERT: D 154 ASP cc_start: 0.7840 (t0) cc_final: 0.7577 (t0) REVERT: E 25 GLN cc_start: 0.8979 (mt0) cc_final: 0.8660 (mt0) REVERT: E 69 MET cc_start: 0.8983 (mtp) cc_final: 0.8686 (mmm) REVERT: E 72 SER cc_start: 0.9002 (m) cc_final: 0.8517 (t) REVERT: E 123 ASP cc_start: 0.8921 (m-30) cc_final: 0.8290 (t0) REVERT: E 129 TYR cc_start: 0.9000 (m-10) cc_final: 0.8718 (m-10) REVERT: E 167 ASP cc_start: 0.9448 (t0) cc_final: 0.8404 (t0) REVERT: E 171 ASN cc_start: 0.9239 (p0) cc_final: 0.9033 (p0) REVERT: F 1 MET cc_start: 0.8701 (tpp) cc_final: 0.8122 (tpp) REVERT: F 21 ASN cc_start: 0.8755 (m-40) cc_final: 0.7629 (t0) REVERT: F 25 ASP cc_start: 0.8937 (m-30) cc_final: 0.8522 (m-30) REVERT: F 35 ASN cc_start: 0.9473 (m-40) cc_final: 0.9108 (m-40) REVERT: F 68 GLN cc_start: 0.9140 (tp-100) cc_final: 0.8713 (mm-40) REVERT: F 76 TYR cc_start: 0.8770 (t80) cc_final: 0.8338 (t80) REVERT: F 88 MET cc_start: 0.9358 (tpp) cc_final: 0.9093 (tpp) REVERT: F 137 LYS cc_start: 0.9476 (ttpt) cc_final: 0.9192 (ttpt) REVERT: F 146 ASP cc_start: 0.9034 (t0) cc_final: 0.8717 (t0) REVERT: F 161 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8656 (tp30) REVERT: G 46 ASN cc_start: 0.9342 (t0) cc_final: 0.9099 (t0) REVERT: G 74 TYR cc_start: 0.8941 (m-80) cc_final: 0.8713 (m-10) REVERT: G 79 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8739 (pp20) REVERT: G 123 ASP cc_start: 0.9011 (t0) cc_final: 0.8684 (t0) REVERT: G 124 LEU cc_start: 0.9253 (mt) cc_final: 0.8924 (mt) REVERT: G 163 ASN cc_start: 0.9489 (m-40) cc_final: 0.8912 (m-40) REVERT: H 1 MET cc_start: 0.9012 (mtt) cc_final: 0.8668 (mpp) REVERT: H 21 ASN cc_start: 0.8885 (m-40) cc_final: 0.8619 (t0) REVERT: H 91 ILE cc_start: 0.9574 (mm) cc_final: 0.9283 (tp) REVERT: H 117 GLU cc_start: 0.9368 (tp30) cc_final: 0.9091 (tp30) REVERT: H 145 ASN cc_start: 0.8142 (m-40) cc_final: 0.7533 (m-40) REVERT: I 9 ILE cc_start: 0.9766 (tp) cc_final: 0.9527 (tp) REVERT: I 47 ASN cc_start: 0.8509 (p0) cc_final: 0.8223 (p0) REVERT: I 51 LEU cc_start: 0.9296 (mt) cc_final: 0.9030 (mt) REVERT: I 60 TYR cc_start: 0.8332 (m-80) cc_final: 0.8128 (m-80) REVERT: I 94 MET cc_start: 0.9120 (mmm) cc_final: 0.8784 (tpp) REVERT: I 98 CYS cc_start: 0.9067 (m) cc_final: 0.8803 (p) REVERT: I 107 MET cc_start: 0.8849 (mmm) cc_final: 0.8563 (tpt) REVERT: I 119 ASN cc_start: 0.9376 (m110) cc_final: 0.9171 (m110) REVERT: I 127 SER cc_start: 0.9491 (p) cc_final: 0.9153 (t) REVERT: I 140 HIS cc_start: 0.9441 (p90) cc_final: 0.9214 (p90) REVERT: I 144 LEU cc_start: 0.8847 (mt) cc_final: 0.8597 (mt) REVERT: I 173 LEU cc_start: 0.9432 (tp) cc_final: 0.8896 (tt) REVERT: J 17 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8697 (mm-30) REVERT: J 35 ASN cc_start: 0.9419 (m110) cc_final: 0.8470 (t0) REVERT: J 112 LEU cc_start: 0.9454 (mp) cc_final: 0.8955 (mm) REVERT: K 2 LYS cc_start: 0.8398 (tmtt) cc_final: 0.8137 (tttm) REVERT: K 21 ASN cc_start: 0.8374 (p0) cc_final: 0.8157 (t0) REVERT: K 33 ARG cc_start: 0.8635 (ttm110) cc_final: 0.8279 (tpm170) REVERT: K 57 GLN cc_start: 0.8796 (pp30) cc_final: 0.8518 (mm-40) REVERT: K 110 TYR cc_start: 0.8571 (m-10) cc_final: 0.8358 (m-80) REVERT: L 7 LYS cc_start: 0.9212 (ttpp) cc_final: 0.8846 (ptmm) REVERT: L 80 ARG cc_start: 0.9198 (mtm-85) cc_final: 0.8940 (mtm-85) REVERT: L 89 GLU cc_start: 0.9153 (pp20) cc_final: 0.8553 (tm-30) REVERT: L 90 ILE cc_start: 0.9109 (mt) cc_final: 0.8480 (mm) REVERT: L 103 ASP cc_start: 0.9337 (m-30) cc_final: 0.9029 (m-30) REVERT: L 146 ASP cc_start: 0.9263 (t0) cc_final: 0.8773 (t0) REVERT: L 148 ASN cc_start: 0.8795 (m-40) cc_final: 0.8488 (m110) REVERT: L 159 MET cc_start: 0.9127 (mmt) cc_final: 0.8893 (mmt) REVERT: L 161 GLU cc_start: 0.9170 (tt0) cc_final: 0.8801 (tp30) REVERT: M 15 GLN cc_start: 0.9443 (mt0) cc_final: 0.9235 (mt0) REVERT: M 57 GLN cc_start: 0.9677 (mm-40) cc_final: 0.9242 (mm-40) REVERT: M 81 LYS cc_start: 0.9095 (tmtt) cc_final: 0.8881 (mtpp) REVERT: M 99 LEU cc_start: 0.9133 (mt) cc_final: 0.8904 (tp) REVERT: M 115 LEU cc_start: 0.9081 (tt) cc_final: 0.8852 (tp) REVERT: M 118 ILE cc_start: 0.9313 (tp) cc_final: 0.9031 (tp) REVERT: M 129 TYR cc_start: 0.8757 (m-80) cc_final: 0.8320 (m-80) REVERT: M 168 TYR cc_start: 0.9095 (t80) cc_final: 0.8719 (t80) REVERT: M 171 ASN cc_start: 0.8455 (p0) cc_final: 0.8022 (p0) REVERT: N 20 THR cc_start: 0.8501 (t) cc_final: 0.8184 (p) REVERT: N 87 ASP cc_start: 0.9319 (m-30) cc_final: 0.8824 (m-30) REVERT: N 88 MET cc_start: 0.9147 (ttp) cc_final: 0.8680 (ttp) REVERT: N 97 TYR cc_start: 0.9103 (m-10) cc_final: 0.8580 (m-80) REVERT: O 19 LEU cc_start: 0.8367 (mm) cc_final: 0.7294 (tp) REVERT: O 27 VAL cc_start: 0.9158 (t) cc_final: 0.8944 (p) REVERT: O 68 THR cc_start: 0.7652 (t) cc_final: 0.7415 (m) REVERT: O 104 THR cc_start: 0.9122 (p) cc_final: 0.8730 (p) REVERT: O 129 TYR cc_start: 0.9017 (m-80) cc_final: 0.8457 (m-80) REVERT: O 131 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8926 (pt0) REVERT: P 2 LEU cc_start: 0.9235 (mp) cc_final: 0.8666 (mp) REVERT: P 97 TYR cc_start: 0.9212 (m-10) cc_final: 0.8737 (m-10) REVERT: P 103 ASP cc_start: 0.8312 (m-30) cc_final: 0.7971 (p0) REVERT: P 113 ASN cc_start: 0.8691 (t0) cc_final: 0.8471 (t0) REVERT: P 124 THR cc_start: 0.9133 (m) cc_final: 0.8866 (p) REVERT: Q 1 MET cc_start: 0.7698 (mmm) cc_final: 0.7346 (mmm) REVERT: Q 2 LYS cc_start: 0.8814 (mmtp) cc_final: 0.8509 (mmtm) REVERT: Q 25 GLN cc_start: 0.9248 (mm-40) cc_final: 0.8744 (mm110) REVERT: Q 39 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7314 (mt-10) REVERT: Q 62 LYS cc_start: 0.6940 (ttmm) cc_final: 0.6712 (ttmm) REVERT: Q 69 MET cc_start: 0.6836 (ptm) cc_final: 0.6520 (ptm) REVERT: Q 94 MET cc_start: 0.6465 (tpp) cc_final: 0.6251 (tpp) REVERT: Q 108 ASP cc_start: 0.9361 (m-30) cc_final: 0.9037 (m-30) REVERT: R 29 ASN cc_start: 0.7465 (t0) cc_final: 0.6805 (m110) REVERT: R 30 LEU cc_start: 0.5960 (mm) cc_final: 0.5723 (mm) REVERT: R 38 LEU cc_start: 0.8719 (mt) cc_final: 0.8271 (mp) REVERT: R 87 ASP cc_start: 0.8204 (m-30) cc_final: 0.7952 (m-30) REVERT: R 88 MET cc_start: 0.9534 (mmm) cc_final: 0.9302 (mtm) REVERT: R 99 ILE cc_start: 0.8906 (mm) cc_final: 0.8623 (mm) REVERT: R 111 CYS cc_start: 0.8745 (t) cc_final: 0.8291 (t) REVERT: R 128 SER cc_start: 0.8557 (m) cc_final: 0.8234 (m) REVERT: R 134 GLN cc_start: 0.8593 (mm-40) cc_final: 0.7990 (mm-40) REVERT: R 136 MET cc_start: 0.9037 (ttp) cc_final: 0.8206 (tmm) REVERT: R 159 MET cc_start: 0.8542 (mmp) cc_final: 0.7741 (ptt) REVERT: S 44 LEU cc_start: 0.9684 (mt) cc_final: 0.9371 (tp) REVERT: S 49 GLN cc_start: 0.9422 (tp-100) cc_final: 0.8726 (pm20) REVERT: S 73 GLN cc_start: 0.8791 (pt0) cc_final: 0.8289 (pm20) REVERT: S 74 TYR cc_start: 0.8906 (m-80) cc_final: 0.8576 (m-80) REVERT: S 97 TYR cc_start: 0.9377 (m-80) cc_final: 0.9058 (m-80) REVERT: S 133 LEU cc_start: 0.9035 (mt) cc_final: 0.8831 (mt) REVERT: S 139 ASN cc_start: 0.9013 (m110) cc_final: 0.8734 (m110) REVERT: T 1 MET cc_start: 0.9211 (tpp) cc_final: 0.7136 (ppp) REVERT: T 9 VAL cc_start: 0.9218 (t) cc_final: 0.8944 (p) REVERT: T 13 ASP cc_start: 0.8977 (t0) cc_final: 0.8419 (t0) REVERT: T 15 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7313 (mmm160) REVERT: T 23 GLN cc_start: 0.8274 (mt0) cc_final: 0.7779 (mp10) REVERT: T 51 ILE cc_start: 0.7353 (mt) cc_final: 0.7148 (mt) REVERT: T 79 ARG cc_start: 0.8557 (tmm-80) cc_final: 0.8290 (tmt-80) REVERT: T 93 ARG cc_start: 0.8769 (ttp-170) cc_final: 0.6763 (tpp80) REVERT: U 33 ARG cc_start: 0.9247 (ttp-110) cc_final: 0.9028 (mtp-110) REVERT: U 65 TYR cc_start: 0.9436 (p90) cc_final: 0.9112 (p90) REVERT: U 109 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8641 (tm-30) REVERT: V 11 GLN cc_start: 0.8907 (tt0) cc_final: 0.8214 (tp40) REVERT: V 33 GLU cc_start: 0.9113 (mp0) cc_final: 0.8733 (mp0) REVERT: V 62 GLU cc_start: 0.9486 (tm-30) cc_final: 0.9245 (tm-30) REVERT: V 67 ILE cc_start: 0.8961 (pt) cc_final: 0.8728 (mt) REVERT: V 68 GLN cc_start: 0.8973 (pt0) cc_final: 0.8705 (pt0) REVERT: V 81 MET cc_start: 0.8488 (tpp) cc_final: 0.7472 (tpp) REVERT: V 150 ILE cc_start: 0.8562 (tt) cc_final: 0.7712 (pt) REVERT: V 159 MET cc_start: 0.9194 (mmp) cc_final: 0.8449 (tmm) REVERT: W 1 MET cc_start: 0.6351 (pmm) cc_final: 0.5794 (pmm) REVERT: W 3 THR cc_start: 0.7820 (m) cc_final: 0.7595 (m) REVERT: W 24 LEU cc_start: 0.9160 (mt) cc_final: 0.8877 (mt) REVERT: W 69 MET cc_start: 0.5566 (mtp) cc_final: 0.5154 (mmm) REVERT: W 94 MET cc_start: 0.9090 (ppp) cc_final: 0.8498 (ppp) REVERT: W 97 TYR cc_start: 0.8182 (m-10) cc_final: 0.7730 (m-80) REVERT: W 111 LEU cc_start: 0.8255 (pt) cc_final: 0.7793 (pp) REVERT: X 38 LEU cc_start: 0.9465 (mt) cc_final: 0.9227 (mt) REVERT: X 52 VAL cc_start: 0.9278 (t) cc_final: 0.9041 (p) REVERT: X 88 MET cc_start: 0.9147 (ttm) cc_final: 0.8753 (ttt) REVERT: X 89 GLU cc_start: 0.9285 (tt0) cc_final: 0.8797 (tm-30) REVERT: X 115 LEU cc_start: 0.8108 (tp) cc_final: 0.7900 (tp) REVERT: X 133 ILE cc_start: 0.8881 (mt) cc_final: 0.8326 (tp) REVERT: X 136 MET cc_start: 0.8215 (mmm) cc_final: 0.7830 (mmm) REVERT: Y 20 PHE cc_start: 0.8588 (m-10) cc_final: 0.8381 (m-10) REVERT: Z 36 ILE cc_start: 0.9117 (mt) cc_final: 0.8868 (pt) REVERT: Z 42 GLN cc_start: 0.9293 (tp40) cc_final: 0.8877 (tp40) REVERT: Z 101 LYS cc_start: 0.9331 (tmtt) cc_final: 0.9091 (ttpp) REVERT: Z 124 GLU cc_start: 0.9373 (tp30) cc_final: 0.9139 (tp30) REVERT: Z 134 ILE cc_start: 0.9282 (mm) cc_final: 0.9073 (mm) REVERT: Z 233 GLU cc_start: 0.7291 (mp0) cc_final: 0.6799 (mp0) REVERT: Z 270 LYS cc_start: 0.9523 (tppt) cc_final: 0.9250 (tttp) REVERT: a 65 GLN cc_start: 0.7915 (tt0) cc_final: 0.7649 (tm-30) REVERT: a 68 LEU cc_start: 0.8350 (mm) cc_final: 0.7811 (mm) REVERT: a 84 ARG cc_start: 0.9028 (ttm110) cc_final: 0.8406 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 1573 average time/residue: 0.4670 time to fit residues: 1190.2890 Evaluate side-chains 1311 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1311 time to evaluate : 3.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 267 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 274 optimal weight: 6.9990 chunk 294 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 40 optimal weight: 0.0170 chunk 339 optimal weight: 0.8980 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN D 29 ASN E 15 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN F 11 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 ASN ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 285 ASN a 161 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.5882 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= 0.214 Angle : 0.739 42.947 49243 Z= 0.347 Chirality : 0.039 0.192 5448 Planarity : 0.004 0.067 6402 Dihedral : 10.964 88.940 6599 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 0.06 % Allowed : 0.94 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.13), residues: 4448 helix: 1.25 (0.09), residues: 3276 sheet: 1.55 (0.74), residues: 28 loop : -0.87 (0.20), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 128 HIS 0.008 0.002 HIS Z 117 PHE 0.032 0.002 PHE Q 31 TYR 0.056 0.002 TYR S 90 ARG 0.011 0.001 ARG T 86 *********************** 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 1614 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1612 time to evaluate : 3.781 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: A 18 PHE cc_start: 0.8162 (m-80) cc_final: 0.7540 (m-10) REVERT: A 62 LYS cc_start: 0.9339 (tptt) cc_final: 0.9010 (tptt) REVERT: A 63 PHE cc_start: 0.9145 (m-80) cc_final: 0.8552 (m-80) REVERT: A 90 TYR cc_start: 0.9048 (m-10) cc_final: 0.8752 (m-80) REVERT: A 167 ASP cc_start: 0.9425 (t0) cc_final: 0.9059 (t0) REVERT: B 32 LYS cc_start: 0.8982 (ttpp) cc_final: 0.8484 (tppt) REVERT: B 36 LYS cc_start: 0.9087 (mtmm) cc_final: 0.8853 (mppt) REVERT: B 81 MET cc_start: 0.8680 (tpp) cc_final: 0.8429 (tpt) REVERT: B 89 GLU cc_start: 0.9430 (pt0) cc_final: 0.8968 (tt0) REVERT: B 103 ASP cc_start: 0.9009 (t0) cc_final: 0.8743 (t0) REVERT: B 108 ASP cc_start: 0.9394 (m-30) cc_final: 0.8857 (m-30) REVERT: B 112 LEU cc_start: 0.9384 (mt) cc_final: 0.8889 (mp) REVERT: B 120 GLN cc_start: 0.8764 (mt0) cc_final: 0.8063 (tm-30) REVERT: B 145 ASN cc_start: 0.8792 (t0) cc_final: 0.8370 (p0) REVERT: B 159 MET cc_start: 0.9311 (mpp) cc_final: 0.8933 (mpp) REVERT: C 69 MET cc_start: 0.7837 (ttm) cc_final: 0.7170 (ttm) REVERT: C 74 TYR cc_start: 0.8349 (m-80) cc_final: 0.7952 (m-80) REVERT: C 94 MET cc_start: 0.9525 (mmt) cc_final: 0.9227 (mmm) REVERT: C 115 LEU cc_start: 0.8887 (pp) cc_final: 0.8652 (pp) REVERT: C 118 ILE cc_start: 0.9285 (tp) cc_final: 0.9040 (tp) REVERT: C 119 ASN cc_start: 0.8644 (m110) cc_final: 0.8056 (p0) REVERT: D 49 SER cc_start: 0.8955 (p) cc_final: 0.8730 (p) REVERT: D 88 MET cc_start: 0.8566 (mmm) cc_final: 0.8350 (mmm) REVERT: D 97 TYR cc_start: 0.9005 (m-10) cc_final: 0.8236 (m-80) REVERT: D 111 CYS cc_start: 0.8872 (t) cc_final: 0.8456 (t) REVERT: D 127 SER cc_start: 0.9236 (p) cc_final: 0.9004 (t) REVERT: D 128 SER cc_start: 0.9433 (p) cc_final: 0.9003 (p) REVERT: D 146 ASP cc_start: 0.9484 (t0) cc_final: 0.9273 (t0) REVERT: D 154 ASP cc_start: 0.7876 (t0) cc_final: 0.7622 (t0) REVERT: D 167 ASP cc_start: 0.9043 (m-30) cc_final: 0.8301 (p0) REVERT: E 25 GLN cc_start: 0.8991 (mt0) cc_final: 0.8624 (mt0) REVERT: E 38 MET cc_start: 0.8872 (mmp) cc_final: 0.8033 (tmm) REVERT: E 72 SER cc_start: 0.8880 (m) cc_final: 0.8393 (t) REVERT: E 94 MET cc_start: 0.8885 (tpp) cc_final: 0.8098 (tpp) REVERT: E 123 ASP cc_start: 0.8920 (m-30) cc_final: 0.8261 (t0) REVERT: E 167 ASP cc_start: 0.9436 (t0) cc_final: 0.8305 (t0) REVERT: F 1 MET cc_start: 0.7877 (tpp) cc_final: 0.7146 (tpp) REVERT: F 21 ASN cc_start: 0.8741 (m-40) cc_final: 0.7631 (t0) REVERT: F 35 ASN cc_start: 0.9424 (m-40) cc_final: 0.9065 (m-40) REVERT: F 68 GLN cc_start: 0.9113 (tp-100) cc_final: 0.8690 (mm110) REVERT: F 76 TYR cc_start: 0.8625 (t80) cc_final: 0.8152 (t80) REVERT: F 146 ASP cc_start: 0.8929 (t0) cc_final: 0.8454 (t0) REVERT: F 161 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8568 (tp30) REVERT: G 5 ILE cc_start: 0.8917 (mp) cc_final: 0.8640 (tt) REVERT: G 7 GLU cc_start: 0.9619 (tp30) cc_final: 0.9367 (mm-30) REVERT: G 46 ASN cc_start: 0.9310 (t0) cc_final: 0.9043 (t0) REVERT: G 74 TYR cc_start: 0.8870 (m-80) cc_final: 0.8655 (m-10) REVERT: G 79 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8716 (pp20) REVERT: G 99 LEU cc_start: 0.9217 (tp) cc_final: 0.8720 (tp) REVERT: G 123 ASP cc_start: 0.9047 (t0) cc_final: 0.8737 (t0) REVERT: G 124 LEU cc_start: 0.9206 (mt) cc_final: 0.8881 (mt) REVERT: G 129 TYR cc_start: 0.9245 (m-80) cc_final: 0.8880 (m-10) REVERT: G 163 ASN cc_start: 0.9472 (m-40) cc_final: 0.9152 (m-40) REVERT: H 3 ASP cc_start: 0.9192 (p0) cc_final: 0.8781 (p0) REVERT: H 21 ASN cc_start: 0.8879 (m-40) cc_final: 0.8605 (t0) REVERT: H 91 ILE cc_start: 0.9548 (mm) cc_final: 0.9293 (tp) REVERT: H 117 GLU cc_start: 0.9365 (tp30) cc_final: 0.9042 (tp30) REVERT: H 173 VAL cc_start: 0.9027 (t) cc_final: 0.8812 (t) REVERT: I 9 ILE cc_start: 0.9638 (tp) cc_final: 0.9345 (tp) REVERT: I 60 TYR cc_start: 0.8282 (m-80) cc_final: 0.7832 (m-80) REVERT: I 94 MET cc_start: 0.9138 (mmm) cc_final: 0.8892 (tpp) REVERT: I 98 CYS cc_start: 0.9011 (m) cc_final: 0.8750 (p) REVERT: I 107 MET cc_start: 0.8870 (mmm) cc_final: 0.8531 (mmp) REVERT: I 111 LEU cc_start: 0.9150 (tp) cc_final: 0.8941 (tp) REVERT: I 127 SER cc_start: 0.9643 (p) cc_final: 0.9164 (p) REVERT: I 140 HIS cc_start: 0.9409 (p90) cc_final: 0.9193 (p90) REVERT: I 173 LEU cc_start: 0.9380 (tp) cc_final: 0.8852 (tt) REVERT: J 17 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8667 (mm-30) REVERT: J 35 ASN cc_start: 0.9389 (m110) cc_final: 0.8399 (t0) REVERT: J 112 LEU cc_start: 0.9411 (mp) cc_final: 0.8929 (mm) REVERT: J 137 LYS cc_start: 0.9142 (ttpt) cc_final: 0.8922 (ptmt) REVERT: K 21 ASN cc_start: 0.8289 (p0) cc_final: 0.8070 (t0) REVERT: K 33 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8176 (tpm170) REVERT: K 51 LEU cc_start: 0.9518 (mp) cc_final: 0.9268 (mm) REVERT: K 57 GLN cc_start: 0.8911 (pp30) cc_final: 0.8657 (mm-40) REVERT: K 65 TYR cc_start: 0.7240 (p90) cc_final: 0.6892 (p90) REVERT: K 109 GLU cc_start: 0.8444 (tp30) cc_final: 0.8238 (tp30) REVERT: K 135 TYR cc_start: 0.8376 (t80) cc_final: 0.8141 (t80) REVERT: L 7 LYS cc_start: 0.9180 (ttpp) cc_final: 0.8800 (ptmm) REVERT: L 18 PHE cc_start: 0.8273 (m-80) cc_final: 0.8040 (m-80) REVERT: L 63 GLN cc_start: 0.9261 (mt0) cc_final: 0.8744 (mm110) REVERT: L 80 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8883 (mtm-85) REVERT: L 89 GLU cc_start: 0.9091 (pp20) cc_final: 0.8564 (tm-30) REVERT: L 90 ILE cc_start: 0.8995 (mt) cc_final: 0.8400 (mm) REVERT: L 103 ASP cc_start: 0.9406 (m-30) cc_final: 0.9060 (m-30) REVERT: L 113 ASN cc_start: 0.9322 (t0) cc_final: 0.8552 (t0) REVERT: L 146 ASP cc_start: 0.9239 (t0) cc_final: 0.8709 (t0) REVERT: L 159 MET cc_start: 0.9073 (mmt) cc_final: 0.8844 (mmt) REVERT: M 53 ASP cc_start: 0.9450 (t0) cc_final: 0.9146 (t0) REVERT: M 57 GLN cc_start: 0.9673 (mm-40) cc_final: 0.9216 (mm-40) REVERT: M 81 LYS cc_start: 0.9019 (tmtt) cc_final: 0.8790 (mtpp) REVERT: M 99 LEU cc_start: 0.9023 (mt) cc_final: 0.8748 (tp) REVERT: M 115 LEU cc_start: 0.8840 (tt) cc_final: 0.8631 (tp) REVERT: M 118 ILE cc_start: 0.9264 (tp) cc_final: 0.8988 (tp) REVERT: M 129 TYR cc_start: 0.8699 (m-80) cc_final: 0.8226 (m-80) REVERT: M 168 TYR cc_start: 0.8952 (t80) cc_final: 0.8614 (t80) REVERT: M 171 ASN cc_start: 0.8477 (p0) cc_final: 0.8000 (p0) REVERT: N 80 ARG cc_start: 0.8900 (mtm-85) cc_final: 0.8237 (mtm-85) REVERT: N 87 ASP cc_start: 0.9293 (m-30) cc_final: 0.8911 (m-30) REVERT: N 88 MET cc_start: 0.8874 (ttp) cc_final: 0.8595 (ttp) REVERT: N 89 GLU cc_start: 0.9258 (pp20) cc_final: 0.8843 (pp20) REVERT: N 97 TYR cc_start: 0.9156 (m-10) cc_final: 0.8546 (m-80) REVERT: N 111 CYS cc_start: 0.9751 (t) cc_final: 0.9532 (t) REVERT: N 136 MET cc_start: 0.8285 (mpp) cc_final: 0.8041 (mtm) REVERT: N 165 TYR cc_start: 0.9198 (m-10) cc_final: 0.8950 (m-10) REVERT: O 19 LEU cc_start: 0.8160 (mm) cc_final: 0.7440 (mt) REVERT: O 27 VAL cc_start: 0.9151 (t) cc_final: 0.8944 (p) REVERT: O 68 THR cc_start: 0.7586 (t) cc_final: 0.7383 (m) REVERT: O 104 THR cc_start: 0.9099 (p) cc_final: 0.8708 (p) REVERT: O 111 LEU cc_start: 0.9328 (tp) cc_final: 0.9123 (tt) REVERT: O 129 TYR cc_start: 0.8996 (m-80) cc_final: 0.8420 (m-80) REVERT: O 131 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8850 (pt0) REVERT: O 165 TYR cc_start: 0.8036 (m-80) cc_final: 0.7808 (m-80) REVERT: P 2 LEU cc_start: 0.9240 (mp) cc_final: 0.8673 (mp) REVERT: P 35 ASN cc_start: 0.9358 (m-40) cc_final: 0.9023 (t0) REVERT: P 39 ASP cc_start: 0.8925 (m-30) cc_final: 0.8641 (m-30) REVERT: P 97 TYR cc_start: 0.9141 (m-10) cc_final: 0.8485 (m-80) REVERT: P 103 ASP cc_start: 0.8278 (m-30) cc_final: 0.7954 (p0) REVERT: P 116 ARG cc_start: 0.8910 (ttm-80) cc_final: 0.8648 (ptm160) REVERT: P 124 THR cc_start: 0.9117 (m) cc_final: 0.8880 (p) REVERT: Q 25 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8719 (mm110) REVERT: Q 39 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7318 (mt-10) REVERT: Q 62 LYS cc_start: 0.6747 (ttmm) cc_final: 0.6358 (ttmm) REVERT: Q 63 PHE cc_start: 0.7769 (m-10) cc_final: 0.7492 (m-10) REVERT: Q 69 MET cc_start: 0.6995 (ptm) cc_final: 0.6665 (ptm) REVERT: Q 94 MET cc_start: 0.6502 (tpp) cc_final: 0.6269 (tpp) REVERT: Q 108 ASP cc_start: 0.9371 (m-30) cc_final: 0.9030 (m-30) REVERT: R 25 ASP cc_start: 0.6586 (m-30) cc_final: 0.6276 (m-30) REVERT: R 29 ASN cc_start: 0.7691 (t0) cc_final: 0.7040 (m-40) REVERT: R 38 LEU cc_start: 0.8698 (mt) cc_final: 0.8222 (mp) REVERT: R 60 PHE cc_start: 0.8566 (m-80) cc_final: 0.8327 (m-80) REVERT: R 87 ASP cc_start: 0.8118 (m-30) cc_final: 0.7896 (m-30) REVERT: R 88 MET cc_start: 0.9531 (mmm) cc_final: 0.8974 (mtm) REVERT: R 92 LEU cc_start: 0.9339 (tt) cc_final: 0.8488 (mm) REVERT: R 111 CYS cc_start: 0.8704 (t) cc_final: 0.8245 (t) REVERT: R 128 SER cc_start: 0.8539 (m) cc_final: 0.8218 (m) REVERT: R 159 MET cc_start: 0.8328 (mmp) cc_final: 0.7739 (ptt) REVERT: S 44 LEU cc_start: 0.9676 (mt) cc_final: 0.9339 (tp) REVERT: S 49 GLN cc_start: 0.9377 (tp-100) cc_final: 0.8675 (pm20) REVERT: S 73 GLN cc_start: 0.8828 (pt0) cc_final: 0.8302 (pm20) REVERT: S 74 TYR cc_start: 0.9167 (m-80) cc_final: 0.8637 (m-80) REVERT: S 83 LYS cc_start: 0.8960 (mmtp) cc_final: 0.8411 (mmtm) REVERT: S 90 TYR cc_start: 0.9185 (m-80) cc_final: 0.8919 (m-10) REVERT: S 97 TYR cc_start: 0.9447 (m-80) cc_final: 0.9104 (m-80) REVERT: S 139 ASN cc_start: 0.8970 (m110) cc_final: 0.8731 (m110) REVERT: T 1 MET cc_start: 0.9190 (tpp) cc_final: 0.7245 (ppp) REVERT: T 9 VAL cc_start: 0.9177 (t) cc_final: 0.8953 (p) REVERT: T 13 ASP cc_start: 0.8891 (t0) cc_final: 0.8507 (t0) REVERT: T 15 ARG cc_start: 0.8113 (mtp85) cc_final: 0.7278 (mmm160) REVERT: T 19 LEU cc_start: 0.8158 (mm) cc_final: 0.7939 (mm) REVERT: T 23 GLN cc_start: 0.8265 (mt0) cc_final: 0.7942 (mp10) REVERT: T 47 ASN cc_start: 0.8113 (t0) cc_final: 0.7847 (t0) REVERT: T 51 ILE cc_start: 0.6900 (mt) cc_final: 0.6548 (mt) REVERT: T 79 ARG cc_start: 0.8546 (tmm-80) cc_final: 0.8306 (tmt-80) REVERT: U 65 TYR cc_start: 0.9429 (p90) cc_final: 0.9089 (p90) REVERT: U 109 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8887 (tm-30) REVERT: V 11 GLN cc_start: 0.8911 (tt0) cc_final: 0.8189 (tp40) REVERT: V 27 LEU cc_start: 0.9353 (mt) cc_final: 0.8999 (mt) REVERT: V 33 GLU cc_start: 0.9167 (mp0) cc_final: 0.8733 (mp0) REVERT: V 62 GLU cc_start: 0.9514 (tm-30) cc_final: 0.9278 (tm-30) REVERT: V 67 ILE cc_start: 0.8913 (pt) cc_final: 0.8689 (mt) REVERT: V 68 GLN cc_start: 0.8965 (pt0) cc_final: 0.8605 (pt0) REVERT: V 150 ILE cc_start: 0.8543 (tt) cc_final: 0.7697 (pt) REVERT: V 159 MET cc_start: 0.9206 (mmp) cc_final: 0.8490 (tmm) REVERT: V 162 ILE cc_start: 0.8998 (mt) cc_final: 0.8781 (mt) REVERT: W 3 THR cc_start: 0.7827 (m) cc_final: 0.7603 (m) REVERT: W 24 LEU cc_start: 0.9106 (mt) cc_final: 0.8896 (mt) REVERT: W 69 MET cc_start: 0.5538 (mtp) cc_final: 0.5125 (mmm) REVERT: W 94 MET cc_start: 0.9276 (ppp) cc_final: 0.8777 (ppp) REVERT: W 97 TYR cc_start: 0.8159 (m-10) cc_final: 0.7823 (m-80) REVERT: W 111 LEU cc_start: 0.8266 (pt) cc_final: 0.7762 (pp) REVERT: X 38 LEU cc_start: 0.9434 (mt) cc_final: 0.9222 (mt) REVERT: X 52 VAL cc_start: 0.9255 (t) cc_final: 0.9036 (p) REVERT: X 77 THR cc_start: 0.7988 (m) cc_final: 0.7611 (p) REVERT: X 88 MET cc_start: 0.9103 (ttm) cc_final: 0.8769 (ttt) REVERT: X 89 GLU cc_start: 0.9274 (tt0) cc_final: 0.8788 (tm-30) REVERT: X 97 TYR cc_start: 0.8466 (m-80) cc_final: 0.7345 (m-80) REVERT: X 133 ILE cc_start: 0.8805 (mt) cc_final: 0.8250 (tp) REVERT: X 166 PHE cc_start: 0.8003 (m-80) cc_final: 0.7607 (m-80) REVERT: Y 20 PHE cc_start: 0.8683 (m-10) cc_final: 0.8478 (m-10) REVERT: Z 36 ILE cc_start: 0.9000 (mt) cc_final: 0.8739 (pt) REVERT: Z 42 GLN cc_start: 0.9033 (tp40) cc_final: 0.8721 (tp40) REVERT: Z 59 GLU cc_start: 0.9096 (mp0) cc_final: 0.8828 (mp0) REVERT: Z 101 LYS cc_start: 0.9281 (tmtt) cc_final: 0.9017 (ttpp) REVERT: Z 124 GLU cc_start: 0.9331 (tp30) cc_final: 0.9032 (tp30) REVERT: Z 134 ILE cc_start: 0.9223 (mm) cc_final: 0.8974 (mm) REVERT: Z 141 ASN cc_start: 0.8805 (m-40) cc_final: 0.8468 (m110) REVERT: Z 192 ARG cc_start: 0.9026 (ttp-110) cc_final: 0.8708 (ttp80) REVERT: Z 270 LYS cc_start: 0.9508 (tppt) cc_final: 0.9243 (tttp) REVERT: a 65 GLN cc_start: 0.8008 (tt0) cc_final: 0.7664 (tm-30) REVERT: a 68 LEU cc_start: 0.8339 (mm) cc_final: 0.7793 (mm) REVERT: a 74 ASN cc_start: 0.9327 (t0) cc_final: 0.8946 (p0) REVERT: a 84 ARG cc_start: 0.8983 (ttm110) cc_final: 0.8739 (ttm110) REVERT: a 129 ILE cc_start: 0.8852 (tt) cc_final: 0.8646 (tp) outliers start: 2 outliers final: 0 residues processed: 1614 average time/residue: 0.4558 time to fit residues: 1187.6106 Evaluate side-chains 1356 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1356 time to evaluate : 3.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 392 optimal weight: 3.9990 chunk 413 optimal weight: 0.0980 chunk 377 optimal weight: 0.2980 chunk 402 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 175 optimal weight: 0.5980 chunk 315 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 363 optimal weight: 0.0570 chunk 380 optimal weight: 0.7980 chunk 400 optimal weight: 10.0000 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN C 46 ASN E 15 GLN F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 ASN ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 163 ASN ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN X 47 ASN ** X 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 64 ASN ** Z 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 GLN a 156 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 36155 Z= 0.190 Angle : 0.742 42.888 49243 Z= 0.346 Chirality : 0.039 0.207 5448 Planarity : 0.004 0.055 6402 Dihedral : 10.836 89.470 6599 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 0.03 % Allowed : 0.74 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.13), residues: 4448 helix: 1.21 (0.09), residues: 3314 sheet: 1.55 (0.82), residues: 28 loop : -0.75 (0.21), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 128 HIS 0.006 0.002 HIS E 140 PHE 0.045 0.002 PHE T 166 TYR 0.045 0.002 TYR R 97 ARG 0.014 0.001 ARG D 15 *********************** 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 1627 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1626 time to evaluate : 4.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.9016 (mt0) cc_final: 0.8049 (mm110) REVERT: A 18 PHE cc_start: 0.8066 (m-80) cc_final: 0.7528 (m-10) REVERT: A 46 ASN cc_start: 0.9321 (m-40) cc_final: 0.9035 (m110) REVERT: A 60 TYR cc_start: 0.9094 (m-80) cc_final: 0.8635 (m-80) REVERT: A 62 LYS cc_start: 0.9307 (tptt) cc_final: 0.9064 (tptp) REVERT: A 63 PHE cc_start: 0.9038 (m-80) cc_final: 0.8557 (m-80) REVERT: A 90 TYR cc_start: 0.9106 (m-10) cc_final: 0.8823 (m-80) REVERT: A 94 MET cc_start: 0.8989 (tpp) cc_final: 0.8462 (tpp) REVERT: A 131 GLU cc_start: 0.9312 (pp20) cc_final: 0.9075 (tm-30) REVERT: A 167 ASP cc_start: 0.8974 (t0) cc_final: 0.8706 (t0) REVERT: B 32 LYS cc_start: 0.8968 (ttpp) cc_final: 0.8515 (tppt) REVERT: B 36 LYS cc_start: 0.9044 (mtmm) cc_final: 0.8836 (mppt) REVERT: B 89 GLU cc_start: 0.9458 (pt0) cc_final: 0.9054 (tt0) REVERT: B 103 ASP cc_start: 0.8938 (t0) cc_final: 0.8444 (t70) REVERT: B 108 ASP cc_start: 0.9515 (m-30) cc_final: 0.9012 (m-30) REVERT: B 120 GLN cc_start: 0.8780 (mt0) cc_final: 0.8104 (tm-30) REVERT: B 137 LYS cc_start: 0.9164 (ttpp) cc_final: 0.8753 (ttpp) REVERT: B 145 ASN cc_start: 0.8704 (t0) cc_final: 0.8302 (p0) REVERT: B 159 MET cc_start: 0.9266 (mpp) cc_final: 0.8863 (mpp) REVERT: C 69 MET cc_start: 0.7880 (ttm) cc_final: 0.7443 (ttm) REVERT: C 94 MET cc_start: 0.9504 (mmt) cc_final: 0.9241 (mmm) REVERT: C 115 LEU cc_start: 0.8829 (pp) cc_final: 0.8447 (pt) REVERT: C 119 ASN cc_start: 0.8567 (m110) cc_final: 0.7951 (p0) REVERT: D 49 SER cc_start: 0.8974 (p) cc_final: 0.8722 (p) REVERT: D 97 TYR cc_start: 0.8886 (m-10) cc_final: 0.8162 (m-80) REVERT: D 111 CYS cc_start: 0.8756 (t) cc_final: 0.8315 (t) REVERT: D 127 SER cc_start: 0.9166 (p) cc_final: 0.8954 (t) REVERT: D 128 SER cc_start: 0.9278 (p) cc_final: 0.8820 (p) REVERT: D 146 ASP cc_start: 0.9496 (t0) cc_final: 0.9218 (t0) REVERT: D 154 ASP cc_start: 0.7853 (t0) cc_final: 0.7621 (t0) REVERT: E 25 GLN cc_start: 0.9018 (mt0) cc_final: 0.8612 (mp10) REVERT: E 38 MET cc_start: 0.8981 (mmp) cc_final: 0.8271 (tmm) REVERT: E 69 MET cc_start: 0.8977 (mtp) cc_final: 0.8469 (ttm) REVERT: E 72 SER cc_start: 0.8735 (m) cc_final: 0.8174 (t) REVERT: E 94 MET cc_start: 0.8947 (tpp) cc_final: 0.8071 (ttm) REVERT: E 123 ASP cc_start: 0.8892 (m-30) cc_final: 0.8154 (t0) REVERT: E 167 ASP cc_start: 0.9341 (t0) cc_final: 0.8268 (t0) REVERT: E 171 ASN cc_start: 0.9213 (p0) cc_final: 0.8926 (p0) REVERT: F 1 MET cc_start: 0.7855 (tpp) cc_final: 0.6984 (tpp) REVERT: F 3 ASP cc_start: 0.9119 (p0) cc_final: 0.8812 (p0) REVERT: F 21 ASN cc_start: 0.8718 (m-40) cc_final: 0.7524 (t0) REVERT: F 25 ASP cc_start: 0.8454 (m-30) cc_final: 0.7737 (m-30) REVERT: F 29 ASN cc_start: 0.9314 (m-40) cc_final: 0.8891 (m-40) REVERT: F 35 ASN cc_start: 0.9363 (m-40) cc_final: 0.9047 (m-40) REVERT: F 68 GLN cc_start: 0.9044 (tp-100) cc_final: 0.8663 (mm110) REVERT: F 76 TYR cc_start: 0.8345 (t80) cc_final: 0.7944 (t80) REVERT: F 146 ASP cc_start: 0.8803 (t0) cc_final: 0.8579 (t0) REVERT: F 161 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8742 (tt0) REVERT: F 165 TYR cc_start: 0.9233 (m-80) cc_final: 0.8720 (m-80) REVERT: G 33 ARG cc_start: 0.8880 (mtp-110) cc_final: 0.8645 (mtm110) REVERT: G 46 ASN cc_start: 0.9279 (t0) cc_final: 0.9017 (t0) REVERT: G 79 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8710 (pp20) REVERT: G 97 TYR cc_start: 0.9357 (m-10) cc_final: 0.9036 (m-10) REVERT: G 99 LEU cc_start: 0.9152 (tp) cc_final: 0.8678 (tp) REVERT: G 123 ASP cc_start: 0.9062 (t0) cc_final: 0.8768 (t70) REVERT: G 124 LEU cc_start: 0.9142 (mt) cc_final: 0.8825 (mt) REVERT: G 127 SER cc_start: 0.9216 (p) cc_final: 0.8915 (p) REVERT: G 163 ASN cc_start: 0.9472 (m-40) cc_final: 0.8904 (m-40) REVERT: H 3 ASP cc_start: 0.9124 (p0) cc_final: 0.8920 (p0) REVERT: H 21 ASN cc_start: 0.8836 (m-40) cc_final: 0.8610 (t0) REVERT: H 27 LEU cc_start: 0.8793 (mm) cc_final: 0.8579 (mt) REVERT: H 91 ILE cc_start: 0.9494 (mm) cc_final: 0.9202 (tp) REVERT: H 112 LEU cc_start: 0.9509 (mt) cc_final: 0.8970 (mt) REVERT: H 117 GLU cc_start: 0.9384 (tp30) cc_final: 0.9043 (tp30) REVERT: I 1 MET cc_start: 0.7161 (mpp) cc_final: 0.6932 (mpp) REVERT: I 9 ILE cc_start: 0.9595 (tp) cc_final: 0.9289 (tp) REVERT: I 60 TYR cc_start: 0.7860 (m-80) cc_final: 0.7331 (m-80) REVERT: I 94 MET cc_start: 0.9101 (mmm) cc_final: 0.8752 (tpp) REVERT: I 98 CYS cc_start: 0.8871 (m) cc_final: 0.8570 (p) REVERT: I 107 MET cc_start: 0.8858 (mmm) cc_final: 0.8591 (mmp) REVERT: I 115 LEU cc_start: 0.9058 (tp) cc_final: 0.8715 (tp) REVERT: I 127 SER cc_start: 0.9382 (p) cc_final: 0.9092 (p) REVERT: I 173 LEU cc_start: 0.9396 (tp) cc_final: 0.8794 (tp) REVERT: J 21 ASN cc_start: 0.8458 (p0) cc_final: 0.8137 (m-40) REVERT: J 35 ASN cc_start: 0.9376 (m110) cc_final: 0.8321 (t0) REVERT: J 112 LEU cc_start: 0.9301 (mp) cc_final: 0.8844 (mm) REVERT: K 1 MET cc_start: 0.8114 (mmp) cc_final: 0.7906 (mmm) REVERT: K 21 ASN cc_start: 0.8303 (p0) cc_final: 0.7956 (t0) REVERT: K 33 ARG cc_start: 0.8473 (ttm110) cc_final: 0.8110 (tpm170) REVERT: K 51 LEU cc_start: 0.9490 (mp) cc_final: 0.9210 (mt) REVERT: K 57 GLN cc_start: 0.8901 (pp30) cc_final: 0.8620 (mm-40) REVERT: K 97 TYR cc_start: 0.8460 (m-10) cc_final: 0.7994 (m-80) REVERT: K 135 TYR cc_start: 0.8341 (t80) cc_final: 0.8086 (t80) REVERT: L 7 LYS cc_start: 0.9151 (ttpp) cc_final: 0.8940 (ptmm) REVERT: L 18 PHE cc_start: 0.8136 (m-80) cc_final: 0.7756 (m-80) REVERT: L 78 ASN cc_start: 0.8283 (t0) cc_final: 0.7853 (t0) REVERT: L 89 GLU cc_start: 0.9037 (pp20) cc_final: 0.8582 (tm-30) REVERT: L 113 ASN cc_start: 0.9231 (t0) cc_final: 0.8338 (t0) REVERT: L 146 ASP cc_start: 0.9176 (t0) cc_final: 0.8600 (t0) REVERT: L 159 MET cc_start: 0.8806 (mmt) cc_final: 0.8584 (mmt) REVERT: M 53 ASP cc_start: 0.9348 (t0) cc_final: 0.8992 (t0) REVERT: M 57 GLN cc_start: 0.9589 (mm-40) cc_final: 0.9095 (mm-40) REVERT: M 69 MET cc_start: 0.9570 (tpt) cc_final: 0.9352 (tpp) REVERT: M 81 LYS cc_start: 0.8928 (tmtt) cc_final: 0.8653 (mtpp) REVERT: M 99 LEU cc_start: 0.9020 (mt) cc_final: 0.8752 (tp) REVERT: M 129 TYR cc_start: 0.8409 (m-80) cc_final: 0.8078 (m-80) REVERT: M 171 ASN cc_start: 0.8527 (p0) cc_final: 0.8295 (p0) REVERT: N 65 GLN cc_start: 0.8109 (pm20) cc_final: 0.7766 (pm20) REVERT: N 89 GLU cc_start: 0.9179 (pp20) cc_final: 0.8845 (pp20) REVERT: N 97 TYR cc_start: 0.9120 (m-10) cc_final: 0.8485 (m-80) REVERT: N 103 ASP cc_start: 0.8528 (t0) cc_final: 0.8244 (t0) REVERT: N 107 LEU cc_start: 0.9434 (tp) cc_final: 0.9155 (tp) REVERT: N 119 TYR cc_start: 0.9413 (m-10) cc_final: 0.8625 (m-10) REVERT: N 165 TYR cc_start: 0.9096 (m-10) cc_final: 0.8895 (m-10) REVERT: O 13 ASP cc_start: 0.9366 (t70) cc_final: 0.9096 (t0) REVERT: O 19 LEU cc_start: 0.7933 (mm) cc_final: 0.7715 (mm) REVERT: O 68 THR cc_start: 0.7733 (t) cc_final: 0.7517 (m) REVERT: O 104 THR cc_start: 0.9039 (p) cc_final: 0.8658 (p) REVERT: O 108 ASP cc_start: 0.8982 (m-30) cc_final: 0.8779 (m-30) REVERT: O 131 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8845 (pt0) REVERT: P 2 LEU cc_start: 0.9233 (mp) cc_final: 0.8642 (mp) REVERT: P 94 TYR cc_start: 0.8701 (m-80) cc_final: 0.8487 (m-10) REVERT: P 97 TYR cc_start: 0.8978 (m-10) cc_final: 0.8301 (m-80) REVERT: P 103 ASP cc_start: 0.8332 (m-30) cc_final: 0.7935 (p0) REVERT: P 113 ASN cc_start: 0.8469 (t0) cc_final: 0.8105 (t0) REVERT: P 124 THR cc_start: 0.9112 (m) cc_final: 0.8848 (p) REVERT: P 134 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8436 (mm110) REVERT: Q 1 MET cc_start: 0.7203 (mmm) cc_final: 0.6791 (tpt) REVERT: Q 25 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8938 (mm-40) REVERT: Q 37 SER cc_start: 0.8165 (m) cc_final: 0.7224 (p) REVERT: Q 38 MET cc_start: 0.5431 (mtm) cc_final: 0.5147 (tpp) REVERT: Q 39 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7321 (pt0) REVERT: Q 62 LYS cc_start: 0.6762 (ttmm) cc_final: 0.6338 (ttmm) REVERT: Q 63 PHE cc_start: 0.7741 (m-10) cc_final: 0.7452 (m-10) REVERT: Q 69 MET cc_start: 0.7031 (ptm) cc_final: 0.6670 (ptm) REVERT: Q 94 MET cc_start: 0.6298 (tpp) cc_final: 0.5780 (tpp) REVERT: Q 98 CYS cc_start: 0.8284 (m) cc_final: 0.7749 (m) REVERT: Q 107 MET cc_start: 0.7424 (mtp) cc_final: 0.6725 (mmm) REVERT: Q 108 ASP cc_start: 0.9354 (m-30) cc_final: 0.8968 (m-30) REVERT: Q 166 ILE cc_start: 0.8246 (tp) cc_final: 0.7958 (tt) REVERT: R 1 MET cc_start: 0.6228 (mmm) cc_final: 0.6009 (mmm) REVERT: R 29 ASN cc_start: 0.7695 (t0) cc_final: 0.7292 (m-40) REVERT: R 38 LEU cc_start: 0.8660 (mt) cc_final: 0.8267 (mp) REVERT: R 87 ASP cc_start: 0.8045 (m-30) cc_final: 0.7814 (m-30) REVERT: R 88 MET cc_start: 0.9506 (mmm) cc_final: 0.9227 (mtm) REVERT: R 92 LEU cc_start: 0.9265 (tt) cc_final: 0.8948 (tt) REVERT: R 111 CYS cc_start: 0.8549 (t) cc_final: 0.8184 (t) REVERT: R 128 SER cc_start: 0.8463 (m) cc_final: 0.8183 (m) REVERT: R 136 MET cc_start: 0.9053 (ttp) cc_final: 0.8078 (tmm) REVERT: R 159 MET cc_start: 0.8295 (mmp) cc_final: 0.7652 (ptt) REVERT: R 166 PHE cc_start: 0.8577 (m-80) cc_final: 0.8307 (m-10) REVERT: S 42 ARG cc_start: 0.7465 (tpp80) cc_final: 0.5778 (ttp-110) REVERT: S 49 GLN cc_start: 0.9352 (tp-100) cc_final: 0.8590 (pm20) REVERT: S 73 GLN cc_start: 0.8978 (pt0) cc_final: 0.8478 (pm20) REVERT: S 74 TYR cc_start: 0.9110 (m-80) cc_final: 0.8615 (m-80) REVERT: S 83 LYS cc_start: 0.8862 (mmtp) cc_final: 0.8382 (mmtm) REVERT: S 90 TYR cc_start: 0.9153 (m-80) cc_final: 0.8880 (m-10) REVERT: S 97 TYR cc_start: 0.9455 (m-80) cc_final: 0.9170 (m-80) REVERT: T 1 MET cc_start: 0.8525 (tpp) cc_final: 0.6264 (ppp) REVERT: T 9 VAL cc_start: 0.9169 (t) cc_final: 0.8931 (p) REVERT: T 13 ASP cc_start: 0.8873 (t0) cc_final: 0.8510 (t0) REVERT: T 15 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7220 (mmt-90) REVERT: T 47 ASN cc_start: 0.8362 (t0) cc_final: 0.8084 (t0) REVERT: T 62 GLU cc_start: 0.8362 (pt0) cc_final: 0.7662 (mm-30) REVERT: T 79 ARG cc_start: 0.8530 (tmm-80) cc_final: 0.8282 (tmt-80) REVERT: T 93 ARG cc_start: 0.8595 (ttp-170) cc_final: 0.6293 (tpp80) REVERT: T 97 TYR cc_start: 0.8985 (m-10) cc_final: 0.8619 (m-10) REVERT: U 31 PHE cc_start: 0.9322 (m-80) cc_final: 0.8854 (m-80) REVERT: U 65 TYR cc_start: 0.9313 (p90) cc_final: 0.8962 (p90) REVERT: U 74 TYR cc_start: 0.8494 (m-80) cc_final: 0.8191 (m-10) REVERT: U 109 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8846 (tm-30) REVERT: U 117 GLU cc_start: 0.9285 (pt0) cc_final: 0.8497 (tp30) REVERT: U 163 ASN cc_start: 0.9124 (m110) cc_final: 0.8847 (m110) REVERT: V 11 GLN cc_start: 0.8986 (tt0) cc_final: 0.8219 (tp40) REVERT: V 27 LEU cc_start: 0.9327 (mt) cc_final: 0.8997 (mt) REVERT: V 41 VAL cc_start: 0.9290 (m) cc_final: 0.9041 (t) REVERT: V 62 GLU cc_start: 0.9488 (tm-30) cc_final: 0.9272 (tm-30) REVERT: V 68 GLN cc_start: 0.9033 (pt0) cc_final: 0.8648 (pt0) REVERT: V 150 ILE cc_start: 0.8496 (tt) cc_final: 0.7653 (pt) REVERT: V 159 MET cc_start: 0.9129 (mmp) cc_final: 0.8487 (tmm) REVERT: W 1 MET cc_start: 0.6463 (pmm) cc_final: 0.6026 (pmm) REVERT: W 3 THR cc_start: 0.7829 (m) cc_final: 0.7598 (m) REVERT: W 32 LYS cc_start: 0.9448 (mttm) cc_final: 0.9245 (tppt) REVERT: W 33 ARG cc_start: 0.8783 (mtp85) cc_final: 0.8466 (ttp-170) REVERT: W 69 MET cc_start: 0.5454 (mtp) cc_final: 0.5065 (mmm) REVERT: W 97 TYR cc_start: 0.8158 (m-10) cc_final: 0.7863 (m-80) REVERT: W 111 LEU cc_start: 0.8235 (pt) cc_final: 0.7671 (pp) REVERT: X 38 LEU cc_start: 0.9424 (mt) cc_final: 0.9124 (mt) REVERT: X 52 VAL cc_start: 0.9219 (t) cc_final: 0.9000 (p) REVERT: X 86 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8393 (ttp80) REVERT: X 89 GLU cc_start: 0.9327 (tt0) cc_final: 0.8862 (tm-30) REVERT: X 93 ARG cc_start: 0.8342 (ttp80) cc_final: 0.8018 (ttp80) REVERT: X 97 TYR cc_start: 0.8253 (m-80) cc_final: 0.7939 (m-80) REVERT: X 115 LEU cc_start: 0.7939 (tp) cc_final: 0.7721 (tp) REVERT: X 136 MET cc_start: 0.7870 (mmm) cc_final: 0.7235 (mmm) REVERT: Z 36 ILE cc_start: 0.8946 (mt) cc_final: 0.8649 (pt) REVERT: Z 42 GLN cc_start: 0.9017 (tp40) cc_final: 0.8714 (tp40) REVERT: Z 124 GLU cc_start: 0.9269 (tp30) cc_final: 0.9067 (tp30) REVERT: Z 134 ILE cc_start: 0.9111 (mm) cc_final: 0.8797 (mm) REVERT: Z 192 ARG cc_start: 0.8935 (ttp-110) cc_final: 0.8688 (ttp80) REVERT: Z 193 ASP cc_start: 0.8306 (p0) cc_final: 0.7092 (t0) REVERT: Z 264 TYR cc_start: 0.9546 (t80) cc_final: 0.8860 (t80) REVERT: Z 270 LYS cc_start: 0.9493 (tppt) cc_final: 0.9217 (tttp) REVERT: a 65 GLN cc_start: 0.8167 (tt0) cc_final: 0.7601 (tm-30) REVERT: a 68 LEU cc_start: 0.8306 (mm) cc_final: 0.7825 (mm) REVERT: a 74 ASN cc_start: 0.9275 (t0) cc_final: 0.8927 (p0) REVERT: a 155 ASP cc_start: 0.9059 (p0) cc_final: 0.8535 (t70) REVERT: a 157 THR cc_start: 0.9392 (m) cc_final: 0.8993 (p) outliers start: 1 outliers final: 0 residues processed: 1627 average time/residue: 0.4792 time to fit residues: 1269.3619 Evaluate side-chains 1347 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1347 time to evaluate : 3.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 264 optimal weight: 4.9990 chunk 425 optimal weight: 10.0000 chunk 259 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 446 optimal weight: 7.9990 chunk 410 optimal weight: 2.9990 chunk 355 optimal weight: 0.0010 chunk 36 optimal weight: 0.9990 chunk 274 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN C 163 ASN E 15 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 ASN ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 139 ASN S 171 ASN ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 ASN ** X 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 36155 Z= 0.229 Angle : 0.761 42.885 49243 Z= 0.359 Chirality : 0.040 0.209 5448 Planarity : 0.004 0.051 6402 Dihedral : 10.852 89.714 6599 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.72 % Favored : 97.19 % Rotamer: Outliers : 0.09 % Allowed : 0.41 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.13), residues: 4448 helix: 1.15 (0.09), residues: 3315 sheet: 1.53 (0.79), residues: 28 loop : -0.76 (0.21), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 128 HIS 0.006 0.002 HIS G 140 PHE 0.025 0.002 PHE Q 31 TYR 0.043 0.002 TYR R 97 ARG 0.008 0.001 ARG Y 64 ********************** 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 1554 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1551 time to evaluate : 3.791 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 15 GLN cc_start: 0.9027 (mt0) cc_final: 0.8033 (mm110) REVERT: A 18 PHE cc_start: 0.8155 (m-80) cc_final: 0.7599 (m-10) REVERT: A 62 LYS cc_start: 0.9348 (tptt) cc_final: 0.9059 (tptp) REVERT: A 63 PHE cc_start: 0.9070 (m-80) cc_final: 0.8549 (m-80) REVERT: A 90 TYR cc_start: 0.9148 (m-10) cc_final: 0.8905 (m-10) REVERT: A 167 ASP cc_start: 0.9054 (t0) cc_final: 0.8836 (t0) REVERT: B 32 LYS cc_start: 0.8982 (ttpp) cc_final: 0.8534 (tppt) REVERT: B 89 GLU cc_start: 0.9425 (pt0) cc_final: 0.9064 (tt0) REVERT: B 103 ASP cc_start: 0.8997 (t0) cc_final: 0.8725 (t0) REVERT: B 108 ASP cc_start: 0.9506 (m-30) cc_final: 0.9165 (m-30) REVERT: B 120 GLN cc_start: 0.8817 (mt0) cc_final: 0.8168 (tm-30) REVERT: B 137 LYS cc_start: 0.9127 (ttpp) cc_final: 0.8573 (ttpp) REVERT: B 145 ASN cc_start: 0.8724 (t0) cc_final: 0.8335 (p0) REVERT: B 159 MET cc_start: 0.9201 (mpp) cc_final: 0.8755 (mpp) REVERT: C 69 MET cc_start: 0.8035 (ttm) cc_final: 0.7507 (ttm) REVERT: C 118 ILE cc_start: 0.9188 (tp) cc_final: 0.8955 (tp) REVERT: C 119 ASN cc_start: 0.8521 (m110) cc_final: 0.7899 (p0) REVERT: C 173 LEU cc_start: 0.8873 (tp) cc_final: 0.8641 (pp) REVERT: D 49 SER cc_start: 0.8974 (p) cc_final: 0.8713 (p) REVERT: D 111 CYS cc_start: 0.8791 (t) cc_final: 0.8340 (t) REVERT: D 128 SER cc_start: 0.9400 (p) cc_final: 0.9024 (p) REVERT: D 154 ASP cc_start: 0.8066 (t0) cc_final: 0.7801 (t0) REVERT: E 25 GLN cc_start: 0.9035 (mt0) cc_final: 0.8615 (mp10) REVERT: E 38 MET cc_start: 0.9007 (mmp) cc_final: 0.8791 (mmt) REVERT: E 69 MET cc_start: 0.9001 (mtp) cc_final: 0.8767 (ttm) REVERT: E 72 SER cc_start: 0.8880 (m) cc_final: 0.8371 (t) REVERT: E 99 LEU cc_start: 0.8978 (tp) cc_final: 0.8759 (tp) REVERT: E 123 ASP cc_start: 0.8846 (m-30) cc_final: 0.8141 (t0) REVERT: E 167 ASP cc_start: 0.9390 (t0) cc_final: 0.8583 (t0) REVERT: F 1 MET cc_start: 0.7800 (tpp) cc_final: 0.6967 (tpp) REVERT: F 3 ASP cc_start: 0.9109 (p0) cc_final: 0.8834 (p0) REVERT: F 21 ASN cc_start: 0.8760 (m-40) cc_final: 0.7568 (t0) REVERT: F 25 ASP cc_start: 0.8497 (m-30) cc_final: 0.8094 (m-30) REVERT: F 35 ASN cc_start: 0.9396 (m-40) cc_final: 0.9072 (m-40) REVERT: F 68 GLN cc_start: 0.9090 (tp-100) cc_final: 0.8674 (mm110) REVERT: F 76 TYR cc_start: 0.8520 (t80) cc_final: 0.8077 (t80) REVERT: F 146 ASP cc_start: 0.8712 (t0) cc_final: 0.8446 (t0) REVERT: F 161 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8756 (tt0) REVERT: F 165 TYR cc_start: 0.9197 (m-80) cc_final: 0.8687 (m-80) REVERT: G 46 ASN cc_start: 0.9233 (t0) cc_final: 0.8975 (t0) REVERT: G 70 GLN cc_start: 0.8837 (pp30) cc_final: 0.8594 (pp30) REVERT: G 79 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8736 (pp20) REVERT: G 97 TYR cc_start: 0.9379 (m-10) cc_final: 0.9008 (m-10) REVERT: G 99 LEU cc_start: 0.9184 (tp) cc_final: 0.8713 (tp) REVERT: G 124 LEU cc_start: 0.9165 (mt) cc_final: 0.8913 (mt) REVERT: G 127 SER cc_start: 0.9260 (p) cc_final: 0.9013 (p) REVERT: G 129 TYR cc_start: 0.9257 (m-80) cc_final: 0.8532 (m-10) REVERT: G 163 ASN cc_start: 0.9552 (m-40) cc_final: 0.9080 (m-40) REVERT: H 1 MET cc_start: 0.8363 (mtt) cc_final: 0.7908 (mpp) REVERT: H 21 ASN cc_start: 0.8791 (m-40) cc_final: 0.8570 (t0) REVERT: H 38 LEU cc_start: 0.9530 (mt) cc_final: 0.8783 (tt) REVERT: H 91 ILE cc_start: 0.9558 (mm) cc_final: 0.9244 (tp) REVERT: H 107 LEU cc_start: 0.9531 (tp) cc_final: 0.9324 (tt) REVERT: H 117 GLU cc_start: 0.9438 (tp30) cc_final: 0.9100 (tp30) REVERT: H 147 PRO cc_start: 0.8642 (Cg_endo) cc_final: 0.8366 (Cg_exo) REVERT: H 159 MET cc_start: 0.8540 (ttm) cc_final: 0.8257 (ttm) REVERT: I 9 ILE cc_start: 0.9622 (tp) cc_final: 0.9316 (tp) REVERT: I 60 TYR cc_start: 0.7934 (m-80) cc_final: 0.7359 (m-80) REVERT: I 63 PHE cc_start: 0.8597 (m-80) cc_final: 0.8190 (m-10) REVERT: I 94 MET cc_start: 0.9102 (mmm) cc_final: 0.8805 (tpp) REVERT: I 98 CYS cc_start: 0.8818 (m) cc_final: 0.8550 (p) REVERT: I 107 MET cc_start: 0.8914 (mmm) cc_final: 0.8548 (mmp) REVERT: I 127 SER cc_start: 0.9362 (p) cc_final: 0.9051 (p) REVERT: I 173 LEU cc_start: 0.9474 (tp) cc_final: 0.8836 (tt) REVERT: J 21 ASN cc_start: 0.8505 (p0) cc_final: 0.8162 (m-40) REVERT: J 35 ASN cc_start: 0.9408 (m110) cc_final: 0.8360 (t0) REVERT: J 68 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8066 (tm-30) REVERT: J 112 LEU cc_start: 0.9283 (mp) cc_final: 0.8814 (mm) REVERT: K 33 ARG cc_start: 0.8460 (ttm110) cc_final: 0.8108 (tpm170) REVERT: K 51 LEU cc_start: 0.9317 (mp) cc_final: 0.9062 (mm) REVERT: K 57 GLN cc_start: 0.8923 (pp30) cc_final: 0.8647 (mm-40) REVERT: K 97 TYR cc_start: 0.8489 (m-10) cc_final: 0.8001 (m-80) REVERT: K 135 TYR cc_start: 0.8411 (t80) cc_final: 0.8142 (t80) REVERT: L 7 LYS cc_start: 0.9182 (ttpp) cc_final: 0.8948 (ptmm) REVERT: L 78 ASN cc_start: 0.8325 (t0) cc_final: 0.8081 (t0) REVERT: L 88 MET cc_start: 0.8262 (ptp) cc_final: 0.7575 (mtm) REVERT: L 89 GLU cc_start: 0.8877 (pp20) cc_final: 0.8607 (tm-30) REVERT: L 113 ASN cc_start: 0.9350 (t0) cc_final: 0.8498 (t0) REVERT: L 146 ASP cc_start: 0.9210 (t0) cc_final: 0.8646 (t0) REVERT: M 57 GLN cc_start: 0.9674 (mm-40) cc_final: 0.9234 (mm-40) REVERT: M 69 MET cc_start: 0.9585 (tpt) cc_final: 0.9302 (tpt) REVERT: M 81 LYS cc_start: 0.8993 (tmtt) cc_final: 0.8747 (mtpp) REVERT: M 94 MET cc_start: 0.9405 (ttm) cc_final: 0.8733 (ttt) REVERT: M 96 THR cc_start: 0.9212 (p) cc_final: 0.8997 (p) REVERT: M 111 LEU cc_start: 0.8790 (tp) cc_final: 0.8505 (tp) REVERT: M 119 ASN cc_start: 0.9066 (p0) cc_final: 0.8840 (p0) REVERT: M 129 TYR cc_start: 0.8553 (m-80) cc_final: 0.8259 (m-80) REVERT: M 139 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8460 (t0) REVERT: M 171 ASN cc_start: 0.8463 (p0) cc_final: 0.8057 (p0) REVERT: N 65 GLN cc_start: 0.8169 (pm20) cc_final: 0.7635 (pm20) REVERT: N 89 GLU cc_start: 0.9180 (pp20) cc_final: 0.8904 (pp20) REVERT: N 97 TYR cc_start: 0.9087 (m-10) cc_final: 0.8438 (m-80) REVERT: N 103 ASP cc_start: 0.8625 (t0) cc_final: 0.8413 (t0) REVERT: N 107 LEU cc_start: 0.9471 (tp) cc_final: 0.9213 (tp) REVERT: N 119 TYR cc_start: 0.9271 (m-10) cc_final: 0.8431 (m-10) REVERT: O 68 THR cc_start: 0.7768 (t) cc_final: 0.7566 (m) REVERT: O 104 THR cc_start: 0.9106 (p) cc_final: 0.8638 (p) REVERT: O 108 ASP cc_start: 0.8885 (m-30) cc_final: 0.8590 (m-30) REVERT: O 131 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8840 (pt0) REVERT: O 168 TYR cc_start: 0.8726 (t80) cc_final: 0.8518 (t80) REVERT: P 2 LEU cc_start: 0.9199 (mp) cc_final: 0.8616 (mp) REVERT: P 97 TYR cc_start: 0.8992 (m-10) cc_final: 0.8369 (m-80) REVERT: P 103 ASP cc_start: 0.8339 (m-30) cc_final: 0.7952 (p0) REVERT: P 134 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8417 (mm-40) REVERT: Q 1 MET cc_start: 0.7365 (mmm) cc_final: 0.7157 (tpt) REVERT: Q 25 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8535 (mm110) REVERT: Q 38 MET cc_start: 0.5586 (mtm) cc_final: 0.5197 (tpp) REVERT: Q 39 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7255 (mt-10) REVERT: Q 62 LYS cc_start: 0.6997 (ttmm) cc_final: 0.6590 (ttmm) REVERT: Q 63 PHE cc_start: 0.7812 (m-10) cc_final: 0.7501 (m-10) REVERT: Q 69 MET cc_start: 0.6983 (ptm) cc_final: 0.6644 (ptm) REVERT: Q 94 MET cc_start: 0.6288 (tpp) cc_final: 0.5921 (tpp) REVERT: Q 108 ASP cc_start: 0.9412 (m-30) cc_final: 0.9024 (m-30) REVERT: Q 166 ILE cc_start: 0.8249 (tp) cc_final: 0.7964 (tt) REVERT: R 1 MET cc_start: 0.6397 (mmm) cc_final: 0.5927 (mmm) REVERT: R 29 ASN cc_start: 0.7734 (t0) cc_final: 0.7081 (m-40) REVERT: R 38 LEU cc_start: 0.8681 (mt) cc_final: 0.8215 (mp) REVERT: R 60 PHE cc_start: 0.8543 (m-80) cc_final: 0.8217 (m-80) REVERT: R 85 LEU cc_start: 0.9708 (mt) cc_final: 0.9276 (tp) REVERT: R 87 ASP cc_start: 0.8161 (m-30) cc_final: 0.7901 (m-30) REVERT: R 111 CYS cc_start: 0.8577 (t) cc_final: 0.8206 (t) REVERT: R 128 SER cc_start: 0.8599 (m) cc_final: 0.8322 (m) REVERT: R 136 MET cc_start: 0.9054 (ttp) cc_final: 0.8084 (tmm) REVERT: R 159 MET cc_start: 0.8665 (mmp) cc_final: 0.7788 (ptt) REVERT: R 166 PHE cc_start: 0.8427 (m-80) cc_final: 0.8217 (m-10) REVERT: S 42 ARG cc_start: 0.7508 (tpp80) cc_final: 0.5800 (ttp-110) REVERT: S 44 LEU cc_start: 0.9680 (mt) cc_final: 0.9347 (tp) REVERT: S 49 GLN cc_start: 0.9323 (tp-100) cc_final: 0.8588 (pm20) REVERT: S 73 GLN cc_start: 0.9006 (pt0) cc_final: 0.8491 (pm20) REVERT: S 74 TYR cc_start: 0.9104 (m-80) cc_final: 0.8582 (m-80) REVERT: S 83 LYS cc_start: 0.8760 (mmtp) cc_final: 0.8290 (mmtm) REVERT: S 90 TYR cc_start: 0.9176 (m-80) cc_final: 0.8887 (m-10) REVERT: S 97 TYR cc_start: 0.9457 (m-80) cc_final: 0.9216 (m-80) REVERT: S 161 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8938 (mm-30) REVERT: S 163 ASN cc_start: 0.9456 (m-40) cc_final: 0.9207 (m-40) REVERT: T 1 MET cc_start: 0.8352 (tpp) cc_final: 0.6439 (ppp) REVERT: T 9 VAL cc_start: 0.9161 (t) cc_final: 0.8948 (p) REVERT: T 15 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7237 (mmt-90) REVERT: T 19 LEU cc_start: 0.8143 (mm) cc_final: 0.7757 (mm) REVERT: T 23 GLN cc_start: 0.8297 (mt0) cc_final: 0.7933 (mp10) REVERT: T 47 ASN cc_start: 0.8224 (t0) cc_final: 0.7895 (t0) REVERT: T 93 ARG cc_start: 0.8734 (ttp-170) cc_final: 0.6654 (tpp80) REVERT: T 97 TYR cc_start: 0.8973 (m-10) cc_final: 0.8605 (m-10) REVERT: U 21 ASN cc_start: 0.8200 (t0) cc_final: 0.7798 (t0) REVERT: U 31 PHE cc_start: 0.9260 (m-80) cc_final: 0.8922 (m-80) REVERT: U 65 TYR cc_start: 0.9353 (p90) cc_final: 0.8987 (p90) REVERT: U 74 TYR cc_start: 0.8455 (m-80) cc_final: 0.8165 (m-10) REVERT: U 117 GLU cc_start: 0.9318 (pt0) cc_final: 0.8496 (tp30) REVERT: U 163 ASN cc_start: 0.9150 (m110) cc_final: 0.8816 (m110) REVERT: V 11 GLN cc_start: 0.8989 (tt0) cc_final: 0.8246 (tp40) REVERT: V 27 LEU cc_start: 0.9300 (mt) cc_final: 0.8971 (mt) REVERT: V 62 GLU cc_start: 0.9485 (tm-30) cc_final: 0.9259 (tm-30) REVERT: V 68 GLN cc_start: 0.8863 (pt0) cc_final: 0.8469 (pt0) REVERT: V 150 ILE cc_start: 0.8493 (tt) cc_final: 0.7635 (pt) REVERT: V 159 MET cc_start: 0.9148 (mmp) cc_final: 0.8601 (tmm) REVERT: W 3 THR cc_start: 0.7803 (m) cc_final: 0.7559 (m) REVERT: W 32 LYS cc_start: 0.9454 (mttm) cc_final: 0.9248 (tppt) REVERT: W 33 ARG cc_start: 0.8770 (mtp85) cc_final: 0.8465 (ttp-170) REVERT: W 61 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7676 (mm-40) REVERT: W 69 MET cc_start: 0.5487 (mtp) cc_final: 0.5081 (mmm) REVERT: W 94 MET cc_start: 0.9359 (ppp) cc_final: 0.8988 (ppp) REVERT: W 97 TYR cc_start: 0.8164 (m-10) cc_final: 0.7844 (m-80) REVERT: W 107 MET cc_start: 0.8504 (mmp) cc_final: 0.8116 (mmp) REVERT: W 111 LEU cc_start: 0.8540 (pt) cc_final: 0.8046 (pp) REVERT: X 38 LEU cc_start: 0.9435 (mt) cc_final: 0.9140 (mt) REVERT: X 52 VAL cc_start: 0.9250 (t) cc_final: 0.9015 (p) REVERT: X 89 GLU cc_start: 0.9357 (tt0) cc_final: 0.8838 (tm-30) REVERT: X 136 MET cc_start: 0.7752 (mmm) cc_final: 0.7323 (mmm) REVERT: X 166 PHE cc_start: 0.7969 (m-80) cc_final: 0.7723 (m-80) REVERT: Z 42 GLN cc_start: 0.8993 (tp40) cc_final: 0.8683 (tp40) REVERT: Z 129 ASP cc_start: 0.8981 (t0) cc_final: 0.8724 (t0) REVERT: Z 134 ILE cc_start: 0.9095 (mm) cc_final: 0.8822 (mm) REVERT: Z 192 ARG cc_start: 0.8968 (ttp-110) cc_final: 0.8673 (ttp80) REVERT: Z 270 LYS cc_start: 0.9506 (tppt) cc_final: 0.9228 (tttp) REVERT: a 65 GLN cc_start: 0.8163 (tt0) cc_final: 0.7761 (tm-30) REVERT: a 68 LEU cc_start: 0.8363 (mm) cc_final: 0.7851 (mm) REVERT: a 74 ASN cc_start: 0.9253 (t0) cc_final: 0.8966 (p0) REVERT: a 149 TYR cc_start: 0.8558 (t80) cc_final: 0.8325 (t80) REVERT: a 157 THR cc_start: 0.9405 (m) cc_final: 0.8999 (p) outliers start: 3 outliers final: 0 residues processed: 1553 average time/residue: 0.4543 time to fit residues: 1145.4088 Evaluate side-chains 1320 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1319 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 282 optimal weight: 0.1980 chunk 378 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 327 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 355 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 365 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN C 163 ASN E 15 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN F 11 GLN ** F 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN ** K 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN M 21 ASN ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 GLN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 139 ASN ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 166 ASN ** Z 272 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 = 0.3532 r_free = 0.3532 target = 0.116276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099605 restraints weight = 92182.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102946 restraints weight = 49001.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105123 restraints weight = 29442.895| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.6453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 36155 Z= 0.206 Angle : 0.756 43.373 49243 Z= 0.355 Chirality : 0.039 0.188 5448 Planarity : 0.004 0.066 6402 Dihedral : 10.838 89.678 6599 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.65 % Favored : 97.21 % Rotamer: Outliers : 0.06 % Allowed : 0.47 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.13), residues: 4448 helix: 1.11 (0.09), residues: 3326 sheet: 1.52 (0.79), residues: 28 loop : -0.75 (0.21), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 128 HIS 0.007 0.002 HIS G 140 PHE 0.038 0.002 PHE T 166 TYR 0.047 0.002 TYR M 97 ARG 0.010 0.001 ARG Y 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16044.62 seconds wall clock time: 284 minutes 57.63 seconds (17097.63 seconds total)