Starting phenix.real_space_refine on Thu Mar 5 10:29:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x6l_33023/03_2026/7x6l_33023.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x6l_33023/03_2026/7x6l_33023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x6l_33023/03_2026/7x6l_33023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x6l_33023/03_2026/7x6l_33023.map" model { file = "/net/cci-nas-00/data/ceres_data/7x6l_33023/03_2026/7x6l_33023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x6l_33023/03_2026/7x6l_33023.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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 102 5.16 5 C 13422 2.51 5 N 3705 2.21 5 O 4257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21486 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "K" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "A" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2461 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 299} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 164} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "J" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "C" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2461 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 299} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 164} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "D" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2461 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 299} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 164} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 4.72, per 1000 atoms: 0.22 Number of scatterers: 21486 At special positions: 0 Unit cell: (175.294, 175.294, 142.344, 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 102 16.00 O 4257 8.00 N 3705 7.00 C 13422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 102 " - pdb=" SG CYS I 107 " distance=2.03 Simple disulfide: pdb=" SG CYS I 157 " - pdb=" SG CYS I 213 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 102 " - pdb=" SG CYS G 107 " distance=2.03 Simple disulfide: pdb=" SG CYS G 157 " - pdb=" SG CYS G 213 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS E 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 107 " distance=2.03 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 277 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 76 " distance=2.03 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 63 sheets defined 15.1% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'I' and resid 204 through 206 No H-bonds generated for 'chain 'I' and resid 204 through 206' Processing helix chain 'K' and resid 121 through 126 removed outlier: 3.600A pdb=" N LYS K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 189 removed outlier: 3.710A pdb=" N GLU K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS K 189 " --> pdb=" O ASP K 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.505A pdb=" N GLY A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.987A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.578A pdb=" N LEU A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 109 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.690A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 54 removed outlier: 4.041A pdb=" N GLN B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 51 " --> pdb=" O GLN B 47 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 124 removed outlier: 3.791A pdb=" N GLU B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 162 through 171 removed outlier: 3.610A pdb=" N ALA B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'J' and resid 121 through 126 removed outlier: 3.511A pdb=" N LEU J 125 " --> pdb=" O SER J 121 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS J 126 " --> pdb=" O ASP J 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 121 through 126' Processing helix chain 'J' and resid 183 through 189 removed outlier: 3.722A pdb=" N GLU J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS J 189 " --> pdb=" O ASP J 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.985A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.615A pdb=" N LEU C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 109 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.692A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 54 removed outlier: 4.043A pdb=" N GLN E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS E 51 " --> pdb=" O GLN E 47 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 124 removed outlier: 3.650A pdb=" N GLU E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E 83 " --> pdb=" O ASP E 79 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 154 removed outlier: 3.501A pdb=" N ILE E 152 " --> pdb=" O CYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 171 removed outlier: 3.624A pdb=" N ALA E 166 " --> pdb=" O TYR E 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN E 168 " --> pdb=" O ASP E 164 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE E 171 " --> pdb=" O LEU E 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.515A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 121 through 126' Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.709A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 73 through 80 removed outlier: 3.984A pdb=" N ASP D 77 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL D 78 " --> pdb=" O HIS D 75 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN D 80 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 116 removed outlier: 3.653A pdb=" N LEU D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG D 109 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.684A pdb=" N GLN D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 54 removed outlier: 4.012A pdb=" N GLN F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS F 51 " --> pdb=" O GLN F 47 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG F 54 " --> pdb=" O GLY F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 124 removed outlier: 3.760A pdb=" N GLU F 81 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA F 101 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 162 through 171 removed outlier: 3.612A pdb=" N ALA F 166 " --> pdb=" O TYR F 162 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN F 168 " --> pdb=" O ASP F 164 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.518A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N CYS I 22 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU I 79 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.678A pdb=" N THR I 124 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR I 94 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL I 126 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA I 92 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N MET I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 97 through 98 removed outlier: 3.899A pdb=" N VAL I 119 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 137 through 140 removed outlier: 3.999A pdb=" N VAL I 201 " --> pdb=" O ALA I 153 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU I 155 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 197 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR I 193 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 137 through 140 removed outlier: 3.999A pdb=" N VAL I 201 " --> pdb=" O ALA I 153 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU I 155 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 197 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR I 193 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 168 through 171 removed outlier: 3.678A pdb=" N THR I 168 " --> pdb=" O ASN I 216 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN I 216 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR I 211 " --> pdb=" O VAL I 228 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS I 226 " --> pdb=" O CYS I 213 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL I 215 " --> pdb=" O VAL I 224 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR I 222 " --> pdb=" O HIS I 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 7 removed outlier: 3.961A pdb=" N CYS K 23 " --> pdb=" O PHE K 71 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.209A pdb=" N VAL K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 114 through 118 removed outlier: 3.747A pdb=" N ASN K 137 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL K 133 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA K 130 " --> pdb=" O LEU K 181 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL K 132 " --> pdb=" O LEU K 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 145 through 150 removed outlier: 3.783A pdb=" N LYS K 149 " --> pdb=" O ALA K 193 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS K 207 " --> pdb=" O CYS K 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.546A pdb=" N GLY B 33 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY B 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 16 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B 25 " --> pdb=" O CYS A 14 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 14 " --> pdb=" O ARG B 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.825A pdb=" N THR A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 34 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AB5, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.583A pdb=" N GLN A 44 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.726A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 58 through 61 removed outlier: 5.692A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 136 through 141 removed outlier: 5.197A pdb=" N CYS A 139 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY A 144 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.735A pdb=" N GLY A 181 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 235 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A 180 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 229 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.735A pdb=" N GLY A 181 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.646A pdb=" N LEU A 164 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 247 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 166 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 245 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 281 through 282 removed outlier: 3.579A pdb=" N ILE A 282 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 302 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.517A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS G 22 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU G 79 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.510A pdb=" N GLY G 10 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR G 124 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR G 94 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 126 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA G 92 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL G 93 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N MET G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TYR G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 97 through 98 removed outlier: 3.915A pdb=" N VAL G 119 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 137 through 140 removed outlier: 4.015A pdb=" N VAL G 201 " --> pdb=" O ALA G 153 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU G 155 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER G 197 " --> pdb=" O CYS G 157 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP G 161 " --> pdb=" O TYR G 193 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR G 193 " --> pdb=" O ASP G 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 198 " --> pdb=" O HIS G 181 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 137 through 140 removed outlier: 4.015A pdb=" N VAL G 201 " --> pdb=" O ALA G 153 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU G 155 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER G 197 " --> pdb=" O CYS G 157 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP G 161 " --> pdb=" O TYR G 193 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR G 193 " --> pdb=" O ASP G 161 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 168 through 171 removed outlier: 3.662A pdb=" N THR G 168 " --> pdb=" O ASN G 216 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN G 216 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR G 211 " --> pdb=" O VAL G 228 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 226 " --> pdb=" O CYS G 213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL G 215 " --> pdb=" O VAL G 224 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR G 222 " --> pdb=" O HIS G 217 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 6 through 7 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.228A pdb=" N VAL J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 114 through 118 removed outlier: 3.714A pdb=" N ASN J 137 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL J 133 " --> pdb=" O PHE J 118 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 130 " --> pdb=" O LEU J 181 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL J 132 " --> pdb=" O LEU J 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 145 through 150 removed outlier: 3.799A pdb=" N LYS J 149 " --> pdb=" O ALA J 193 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR J 192 " --> pdb=" O PHE J 209 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS J 207 " --> pdb=" O CYS J 194 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 31 through 35 removed outlier: 3.545A pdb=" N GLY E 33 " --> pdb=" O HIS E 26 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY E 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY C 16 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG E 25 " --> pdb=" O CYS C 14 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS C 14 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.832A pdb=" N THR C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 34 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD8, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.544A pdb=" N GLN C 44 " --> pdb=" O PHE C 294 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.712A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 58 through 61 removed outlier: 5.706A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 136 through 141 removed outlier: 5.217A pdb=" N CYS C 139 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY C 144 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.755A pdb=" N GLY C 181 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 235 " --> pdb=" O TYR C 178 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP C 180 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 229 " --> pdb=" O HIS C 184 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.755A pdb=" N GLY C 181 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.691A pdb=" N VAL C 166 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 245 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 281 through 282 removed outlier: 3.656A pdb=" N ILE C 282 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 302 " --> pdb=" O ILE C 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.521A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.685A pdb=" N THR H 124 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR H 94 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL H 126 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA H 92 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 97 through 98 removed outlier: 3.923A pdb=" N VAL H 119 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 137 through 140 removed outlier: 4.012A pdb=" N VAL H 201 " --> pdb=" O ALA H 153 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU H 155 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H 197 " --> pdb=" O CYS H 157 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP H 161 " --> pdb=" O TYR H 193 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 137 through 140 removed outlier: 4.012A pdb=" N VAL H 201 " --> pdb=" O ALA H 153 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU H 155 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H 197 " --> pdb=" O CYS H 157 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP H 161 " --> pdb=" O TYR H 193 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 168 through 171 removed outlier: 3.689A pdb=" N THR H 168 " --> pdb=" O ASN H 216 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN H 216 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR H 211 " --> pdb=" O VAL H 228 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS H 226 " --> pdb=" O CYS H 213 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 215 " --> pdb=" O VAL H 224 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR H 222 " --> pdb=" O HIS H 217 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 6 through 7 removed outlier: 3.886A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.218A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.708A pdb=" N ASN L 137 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA L 130 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL L 132 " --> pdb=" O LEU L 179 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 145 through 150 removed outlier: 3.790A pdb=" N LYS L 149 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 31 through 35 removed outlier: 3.589A pdb=" N GLY F 33 " --> pdb=" O HIS F 26 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY F 23 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 16 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG F 25 " --> pdb=" O CYS D 14 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS D 14 " --> pdb=" O ARG F 25 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 24 through 26 removed outlier: 3.832A pdb=" N THR D 24 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 34 " --> pdb=" O VAL D 26 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AG2, first strand: chain 'D' and resid 43 through 44 removed outlier: 3.564A pdb=" N GLN D 44 " --> pdb=" O PHE D 294 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 51 through 54 removed outlier: 5.710A pdb=" N ILE D 51 " --> pdb=" O ASP D 275 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N CYS D 277 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN D 53 " --> pdb=" O CYS D 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'D' and resid 58 through 61 removed outlier: 5.700A pdb=" N PHE D 87 " --> pdb=" O MET D 268 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 136 through 141 removed outlier: 5.177A pdb=" N CYS D 139 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY D 144 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.788A pdb=" N GLY D 181 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE D 179 " --> pdb=" O PRO D 254 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 235 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP D 180 " --> pdb=" O TYR D 233 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 229 " --> pdb=" O HIS D 184 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.788A pdb=" N GLY D 181 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE D 179 " --> pdb=" O PRO D 254 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 166 through 169 removed outlier: 3.693A pdb=" N VAL D 166 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D 245 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 281 through 282 removed outlier: 3.553A pdb=" N ILE D 282 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR D 302 " --> pdb=" O ILE D 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 653 hydrogen bonds defined for protein. 1797 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: 3.72 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3618 1.32 - 1.44: 6018 1.44 - 1.57: 12174 1.57 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 21945 Sorted by residual: bond pdb=" C PRO A 324 " pdb=" O PRO A 324 " ideal model delta sigma weight residual 1.235 1.194 0.041 1.30e-02 5.92e+03 9.96e+00 bond pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 1.469 1.442 0.026 1.28e-02 6.10e+03 4.19e+00 bond pdb=" CA PRO A 324 " pdb=" C PRO A 324 " ideal model delta sigma weight residual 1.520 1.498 0.021 1.42e-02 4.96e+03 2.26e+00 bond pdb=" C LYS H 218 " pdb=" N PRO H 219 " ideal model delta sigma weight residual 1.337 1.352 -0.016 1.06e-02 8.90e+03 2.23e+00 bond pdb=" CA PRO A 324 " pdb=" CB PRO A 324 " ideal model delta sigma weight residual 1.533 1.513 0.020 1.42e-02 4.96e+03 2.05e+00 ... (remaining 21940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 29380 1.49 - 2.98: 358 2.98 - 4.48: 37 4.48 - 5.97: 8 5.97 - 7.46: 7 Bond angle restraints: 29790 Sorted by residual: angle pdb=" C SER J 67 " pdb=" CA SER J 67 " pdb=" CB SER J 67 " ideal model delta sigma weight residual 116.54 110.06 6.48 1.46e+00 4.69e-01 1.97e+01 angle pdb=" C PRO A 324 " pdb=" N GLU A 325 " pdb=" CA GLU A 325 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C VAL A 323 " pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 119.84 116.15 3.69 1.25e+00 6.40e-01 8.70e+00 angle pdb=" CA SER J 67 " pdb=" C SER J 67 " pdb=" N GLY J 68 " ideal model delta sigma weight residual 118.57 116.17 2.40 8.80e-01 1.29e+00 7.41e+00 angle pdb=" CA LYS H 218 " pdb=" C LYS H 218 " pdb=" N PRO H 219 " ideal model delta sigma weight residual 118.44 122.36 -3.92 1.59e+00 3.96e-01 6.08e+00 ... (remaining 29785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 12808 17.48 - 34.96: 305 34.96 - 52.44: 41 52.44 - 69.93: 7 69.93 - 87.41: 3 Dihedral angle restraints: 13164 sinusoidal: 5175 harmonic: 7989 Sorted by residual: dihedral pdb=" CA PRO A 324 " pdb=" C PRO A 324 " pdb=" N GLU A 325 " pdb=" CA GLU A 325 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" N CYS D 76 " pdb=" CA CYS D 76 " pdb=" CB CYS D 76 " pdb=" SG CYS D 76 " ideal model delta sinusoidal sigma weight residual 60.00 1.20 58.80 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N CYS A 76 " pdb=" CA CYS A 76 " pdb=" CB CYS A 76 " pdb=" SG CYS A 76 " ideal model delta sinusoidal sigma weight residual 60.00 1.32 58.68 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 13161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2701 0.048 - 0.096: 394 0.096 - 0.144: 210 0.144 - 0.191: 3 0.191 - 0.239: 1 Chirality restraints: 3309 Sorted by residual: chirality pdb=" CA PRO A 324 " pdb=" N PRO A 324 " pdb=" C PRO A 324 " pdb=" CB PRO A 324 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA LYS G 218 " pdb=" N LYS G 218 " pdb=" C LYS G 218 " pdb=" CB LYS G 218 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA LYS I 218 " pdb=" N LYS I 218 " pdb=" C LYS I 218 " pdb=" CB LYS I 218 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 3306 not shown) Planarity restraints: 3876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 323 " 0.086 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO A 324 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 323 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C VAL A 323 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 323 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO A 324 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 238 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 239 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 239 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 239 " -0.021 5.00e-02 4.00e+02 ... (remaining 3873 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6063 2.81 - 3.33: 15982 3.33 - 3.86: 36058 3.86 - 4.38: 39232 4.38 - 4.90: 69614 Nonbonded interactions: 166949 Sorted by model distance: nonbonded pdb=" OG1 THR A 283 " pdb=" O GLY A 286 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR D 283 " pdb=" O GLY D 286 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR C 283 " pdb=" O GLY C 286 " model vdw 2.294 3.040 nonbonded pdb=" O GLU E 103 " pdb=" OG1 THR E 107 " model vdw 2.309 3.040 nonbonded pdb=" O GLU B 103 " pdb=" OG1 THR B 107 " model vdw 2.310 3.040 ... (remaining 166944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.650 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.310 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 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 : 0.002 0.041 21978 Z= 0.107 Angle : 0.447 7.459 29856 Z= 0.261 Chirality : 0.041 0.239 3309 Planarity : 0.005 0.133 3876 Dihedral : 7.433 87.406 7953 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.92 % Favored : 97.89 % Rotamer: Outliers : 2.04 % Allowed : 2.37 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.13), residues: 2754 helix: -4.45 (0.08), residues: 303 sheet: -1.05 (0.17), residues: 807 loop : -2.13 (0.13), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 170 TYR 0.007 0.001 TYR L 49 PHE 0.008 0.001 PHE B 63 TRP 0.005 0.001 TRP C 180 HIS 0.002 0.000 HIS I 217 Details of bonding type rmsd covalent geometry : bond 0.00196 (21945) covalent geometry : angle 0.44681 (29790) SS BOND : bond 0.00121 ( 33) SS BOND : angle 0.37493 ( 66) hydrogen bonds : bond 0.32610 ( 616) hydrogen bonds : angle 10.98392 ( 1797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 694 time to evaluate : 0.859 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: I 77 ASN cc_start: 0.5182 (m-40) cc_final: 0.4658 (p0) REVERT: I 115 TYR cc_start: 0.5421 (m-80) cc_final: 0.5185 (m-80) REVERT: I 161 ASP cc_start: 0.8056 (m-30) cc_final: 0.7814 (p0) REVERT: I 181 HIS cc_start: 0.6415 (m-70) cc_final: 0.5943 (m-70) REVERT: I 195 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6766 (pp) REVERT: I 212 ILE cc_start: 0.6421 (mt) cc_final: 0.6011 (tp) REVERT: K 82 ASP cc_start: 0.6856 (m-30) cc_final: 0.6268 (t0) REVERT: K 139 PHE cc_start: 0.4856 (p90) cc_final: 0.4613 (p90) REVERT: K 172 THR cc_start: 0.8220 (p) cc_final: 0.7973 (m) REVERT: K 210 ASN cc_start: 0.7934 (t0) cc_final: 0.7696 (p0) REVERT: A 75 HIS cc_start: 0.7027 (m-70) cc_final: 0.6587 (m-70) REVERT: A 119 GLU cc_start: 0.7073 (tt0) cc_final: 0.6357 (tt0) REVERT: A 121 ILE cc_start: 0.8385 (mp) cc_final: 0.8158 (mm) REVERT: A 177 LEU cc_start: 0.6891 (tp) cc_final: 0.5997 (mp) REVERT: A 208 ARG cc_start: 0.7141 (mtt90) cc_final: 0.6846 (mtt90) REVERT: A 223 VAL cc_start: 0.7540 (t) cc_final: 0.7156 (p) REVERT: B 25 ARG cc_start: 0.7102 (tmt170) cc_final: 0.6882 (tmt170) REVERT: B 79 ASP cc_start: 0.6202 (m-30) cc_final: 0.5957 (m-30) REVERT: B 85 GLU cc_start: 0.7158 (tp30) cc_final: 0.6613 (tp30) REVERT: B 89 ILE cc_start: 0.8148 (mt) cc_final: 0.7797 (mt) REVERT: B 94 TYR cc_start: 0.7567 (t80) cc_final: 0.7219 (t80) REVERT: B 121 LYS cc_start: 0.7949 (ttpt) cc_final: 0.7616 (tptp) REVERT: G 77 ASN cc_start: 0.4696 (m-40) cc_final: 0.4434 (p0) REVERT: G 115 TYR cc_start: 0.4746 (m-80) cc_final: 0.4396 (m-10) REVERT: G 171 TRP cc_start: 0.6104 (m100) cc_final: 0.5806 (m100) REVERT: J 62 PHE cc_start: 0.6179 (m-80) cc_final: 0.5964 (m-80) REVERT: J 95 PRO cc_start: 0.7596 (Cg_endo) cc_final: 0.7105 (Cg_exo) REVERT: J 139 PHE cc_start: 0.5018 (p90) cc_final: 0.4530 (p90) REVERT: J 172 THR cc_start: 0.8308 (p) cc_final: 0.8067 (m) REVERT: C 40 THR cc_start: 0.8276 (t) cc_final: 0.8004 (p) REVERT: C 50 LYS cc_start: 0.7092 (mttt) cc_final: 0.6758 (mttt) REVERT: C 60 ASP cc_start: 0.7753 (t0) cc_final: 0.7379 (t0) REVERT: C 75 HIS cc_start: 0.6902 (m-70) cc_final: 0.6547 (m-70) REVERT: C 83 THR cc_start: 0.7836 (p) cc_final: 0.6803 (p) REVERT: C 92 LYS cc_start: 0.8391 (pttp) cc_final: 0.8164 (pttp) REVERT: C 117 THR cc_start: 0.8670 (t) cc_final: 0.8012 (m) REVERT: C 119 GLU cc_start: 0.7207 (tt0) cc_final: 0.6528 (tt0) REVERT: C 121 ILE cc_start: 0.8807 (mp) cc_final: 0.8422 (mm) REVERT: C 182 VAL cc_start: 0.5160 (t) cc_final: 0.4439 (t) REVERT: C 184 HIS cc_start: 0.6233 (m-70) cc_final: 0.5990 (m-70) REVERT: C 208 ARG cc_start: 0.7100 (mtt90) cc_final: 0.6576 (mtt90) REVERT: C 213 ILE cc_start: 0.8320 (mm) cc_final: 0.8090 (mm) REVERT: C 223 VAL cc_start: 0.7528 (t) cc_final: 0.7201 (p) REVERT: C 245 ILE cc_start: 0.8808 (mt) cc_final: 0.8553 (mp) REVERT: C 261 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6803 (mtt180) REVERT: C 268 MET cc_start: 0.7864 (ttm) cc_final: 0.7648 (ttm) REVERT: C 275 ASP cc_start: 0.7304 (t0) cc_final: 0.7067 (t0) REVERT: C 307 LYS cc_start: 0.5150 (mttp) cc_final: 0.4786 (mttp) REVERT: E 25 ARG cc_start: 0.6886 (tmt170) cc_final: 0.6653 (tmt170) REVERT: E 49 ASN cc_start: 0.6907 (t0) cc_final: 0.6666 (t0) REVERT: E 79 ASP cc_start: 0.5941 (m-30) cc_final: 0.5670 (m-30) REVERT: E 81 GLU cc_start: 0.6610 (pt0) cc_final: 0.6226 (pt0) REVERT: E 85 GLU cc_start: 0.6806 (tp30) cc_final: 0.6473 (tp30) REVERT: E 90 ASP cc_start: 0.6783 (m-30) cc_final: 0.6523 (m-30) REVERT: E 91 LEU cc_start: 0.8012 (mt) cc_final: 0.7471 (mt) REVERT: E 95 ASN cc_start: 0.7771 (m-40) cc_final: 0.7422 (m-40) REVERT: E 102 LEU cc_start: 0.7695 (tp) cc_final: 0.7433 (tp) REVERT: E 114 GLU cc_start: 0.6419 (mm-30) cc_final: 0.5795 (mm-30) REVERT: H 12 VAL cc_start: 0.8199 (OUTLIER) cc_final: 0.7995 (t) REVERT: H 29 PHE cc_start: 0.7497 (t80) cc_final: 0.6502 (t80) REVERT: H 126 VAL cc_start: 0.6339 (t) cc_final: 0.5974 (p) REVERT: H 195 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6511 (pp) REVERT: L 18 ARG cc_start: 0.7172 (ttm170) cc_final: 0.6949 (ttm170) REVERT: L 73 LEU cc_start: 0.6923 (tp) cc_final: 0.6699 (tp) REVERT: L 139 PHE cc_start: 0.5220 (p90) cc_final: 0.4939 (p90) REVERT: L 180 THR cc_start: 0.7554 (m) cc_final: 0.7322 (t) REVERT: L 210 ASN cc_start: 0.7508 (t0) cc_final: 0.7161 (p0) REVERT: D 50 LYS cc_start: 0.7197 (mttt) cc_final: 0.6636 (mtmm) REVERT: D 53 ASN cc_start: 0.6638 (p0) cc_final: 0.6384 (t0) REVERT: D 57 ARG cc_start: 0.7519 (ttt90) cc_final: 0.6416 (ttt90) REVERT: D 60 ASP cc_start: 0.7428 (t0) cc_final: 0.7192 (t0) REVERT: D 74 PRO cc_start: 0.7170 (Cg_exo) cc_final: 0.6292 (Cg_endo) REVERT: D 75 HIS cc_start: 0.7133 (m-70) cc_final: 0.6850 (m-70) REVERT: D 77 ASP cc_start: 0.7573 (m-30) cc_final: 0.7086 (m-30) REVERT: D 83 THR cc_start: 0.7463 (p) cc_final: 0.5561 (t) REVERT: D 121 ILE cc_start: 0.8784 (mp) cc_final: 0.8509 (mm) REVERT: D 152 ASN cc_start: 0.4798 (t0) cc_final: 0.3988 (t0) REVERT: D 164 LEU cc_start: 0.6987 (mt) cc_final: 0.6747 (pp) REVERT: D 184 HIS cc_start: 0.6148 (m-70) cc_final: 0.5811 (m-70) REVERT: D 186 SER cc_start: 0.7695 (p) cc_final: 0.7389 (m) REVERT: D 207 ARG cc_start: 0.6404 (mtt180) cc_final: 0.5937 (mmm-85) REVERT: F 79 ASP cc_start: 0.6171 (m-30) cc_final: 0.5915 (m-30) REVERT: F 85 GLU cc_start: 0.6816 (tp30) cc_final: 0.6051 (tp30) REVERT: F 89 ILE cc_start: 0.7915 (mt) cc_final: 0.7485 (mt) REVERT: F 91 LEU cc_start: 0.7966 (mt) cc_final: 0.7622 (mt) REVERT: F 94 TYR cc_start: 0.8044 (t80) cc_final: 0.7789 (t80) outliers start: 49 outliers final: 14 residues processed: 730 average time/residue: 0.1626 time to fit residues: 180.2207 Evaluate side-chains 589 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 572 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN K 90 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 GLN A 44 GLN A 53 ASN A 56 HIS A 290 ASN B 64 HIS B 95 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN G 188 GLN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN C 54 ASN C 250 ASN C 285 ASN E 64 HIS E 104 ASN E 106 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN L 160 GLN D 44 GLN D 285 ASN F 64 HIS F 95 ASN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.181564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.155341 restraints weight = 36414.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.161134 restraints weight = 17678.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.164954 restraints weight = 10027.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.167369 restraints weight = 6303.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.168978 restraints weight = 4340.596| |-----------------------------------------------------------------------------| r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 21978 Z= 0.211 Angle : 0.664 12.181 29856 Z= 0.347 Chirality : 0.046 0.207 3309 Planarity : 0.005 0.073 3876 Dihedral : 4.466 54.362 3019 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 2.66 % Allowed : 8.27 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.14), residues: 2754 helix: -1.81 (0.22), residues: 351 sheet: -0.80 (0.18), residues: 783 loop : -1.61 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 150 TYR 0.025 0.002 TYR B 141 PHE 0.033 0.002 PHE B 63 TRP 0.029 0.002 TRP L 148 HIS 0.010 0.002 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00459 (21945) covalent geometry : angle 0.65998 (29790) SS BOND : bond 0.00454 ( 33) SS BOND : angle 1.60540 ( 66) hydrogen bonds : bond 0.05067 ( 616) hydrogen bonds : angle 6.94580 ( 1797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 622 time to evaluate : 0.694 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: I 22 CYS cc_start: 0.5555 (t) cc_final: 0.5030 (t) REVERT: I 79 LEU cc_start: 0.7864 (mt) cc_final: 0.7626 (mm) REVERT: I 83 MET cc_start: 0.5273 (mtp) cc_final: 0.4733 (mtp) REVERT: I 104 SER cc_start: 0.8390 (t) cc_final: 0.8142 (t) REVERT: I 110 VAL cc_start: 0.8032 (t) cc_final: 0.7807 (m) REVERT: I 117 MET cc_start: 0.7044 (mtm) cc_final: 0.6260 (mtt) REVERT: I 181 HIS cc_start: 0.6171 (m-70) cc_final: 0.5513 (m-70) REVERT: K 62 PHE cc_start: 0.7505 (t80) cc_final: 0.7220 (t80) REVERT: K 172 THR cc_start: 0.8286 (p) cc_final: 0.8053 (m) REVERT: K 176 SER cc_start: 0.7403 (t) cc_final: 0.7015 (p) REVERT: K 210 ASN cc_start: 0.8310 (t0) cc_final: 0.8010 (p0) REVERT: A 57 ARG cc_start: 0.7732 (ttt90) cc_final: 0.6787 (ttt90) REVERT: A 75 HIS cc_start: 0.7213 (m-70) cc_final: 0.6684 (m-70) REVERT: A 119 GLU cc_start: 0.7351 (tt0) cc_final: 0.6551 (tt0) REVERT: A 121 ILE cc_start: 0.8272 (mp) cc_final: 0.7932 (mm) REVERT: A 123 GLU cc_start: 0.6441 (mm-30) cc_final: 0.5972 (mm-30) REVERT: A 150 ARG cc_start: 0.7966 (mmm160) cc_final: 0.7742 (mmm160) REVERT: A 223 VAL cc_start: 0.7594 (t) cc_final: 0.7187 (p) REVERT: A 257 TYR cc_start: 0.6828 (p90) cc_final: 0.6539 (p90) REVERT: A 261 ARG cc_start: 0.7542 (mtt180) cc_final: 0.7328 (mtt90) REVERT: A 275 ASP cc_start: 0.7134 (t70) cc_final: 0.6840 (t0) REVERT: A 310 LYS cc_start: 0.7354 (mttt) cc_final: 0.7031 (mtmm) REVERT: B 22 TYR cc_start: 0.6600 (m-80) cc_final: 0.6305 (m-80) REVERT: B 25 ARG cc_start: 0.7070 (tmt170) cc_final: 0.6827 (tmt170) REVERT: B 79 ASP cc_start: 0.7310 (m-30) cc_final: 0.6962 (m-30) REVERT: B 85 GLU cc_start: 0.7699 (tp30) cc_final: 0.7097 (tp30) REVERT: B 89 ILE cc_start: 0.8418 (mt) cc_final: 0.8052 (mt) REVERT: B 94 TYR cc_start: 0.8229 (t80) cc_final: 0.7618 (t80) REVERT: B 121 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7790 (tptp) REVERT: B 133 MET cc_start: 0.5527 (OUTLIER) cc_final: 0.5213 (ptm) REVERT: G 20 LEU cc_start: 0.7922 (mt) cc_final: 0.7685 (mt) REVERT: G 51 ILE cc_start: 0.6647 (tt) cc_final: 0.6158 (mm) REVERT: G 83 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4867 (mtp) REVERT: G 94 TYR cc_start: 0.3822 (m-80) cc_final: 0.3439 (m-80) REVERT: J 27 GLN cc_start: 0.7020 (pp30) cc_final: 0.6735 (pp30) REVERT: J 29 ILE cc_start: 0.7554 (pt) cc_final: 0.7268 (tt) REVERT: J 62 PHE cc_start: 0.6343 (m-80) cc_final: 0.6026 (m-80) REVERT: J 74 THR cc_start: 0.6912 (m) cc_final: 0.6330 (m) REVERT: J 139 PHE cc_start: 0.5118 (p90) cc_final: 0.4606 (p90) REVERT: J 172 THR cc_start: 0.8290 (p) cc_final: 0.8040 (m) REVERT: J 189 HIS cc_start: 0.7679 (m-70) cc_final: 0.7464 (m-70) REVERT: C 50 LYS cc_start: 0.7297 (mttt) cc_final: 0.6668 (mtmm) REVERT: C 92 LYS cc_start: 0.8497 (pttp) cc_final: 0.8139 (pttp) REVERT: C 100 TYR cc_start: 0.7236 (p90) cc_final: 0.7014 (p90) REVERT: C 109 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7618 (mtp180) REVERT: C 119 GLU cc_start: 0.7528 (tt0) cc_final: 0.6680 (tt0) REVERT: C 121 ILE cc_start: 0.8654 (mp) cc_final: 0.8387 (mm) REVERT: C 123 GLU cc_start: 0.5152 (mt-10) cc_final: 0.4880 (mt-10) REVERT: C 161 TYR cc_start: 0.6563 (t80) cc_final: 0.6017 (t80) REVERT: C 184 HIS cc_start: 0.6347 (m-70) cc_final: 0.6015 (m-70) REVERT: C 208 ARG cc_start: 0.7140 (mtt90) cc_final: 0.6609 (mtt90) REVERT: C 245 ILE cc_start: 0.8445 (mt) cc_final: 0.8231 (mp) REVERT: C 260 MET cc_start: 0.7075 (mmm) cc_final: 0.6704 (mmp) REVERT: C 269 ARG cc_start: 0.7629 (mmm-85) cc_final: 0.7421 (mtt90) REVERT: E 78 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6697 (mp10) REVERT: E 79 ASP cc_start: 0.7056 (m-30) cc_final: 0.6721 (m-30) REVERT: E 81 GLU cc_start: 0.7586 (pt0) cc_final: 0.7157 (pt0) REVERT: E 85 GLU cc_start: 0.7342 (tp30) cc_final: 0.7021 (tp30) REVERT: E 91 LEU cc_start: 0.8238 (mt) cc_final: 0.7663 (mt) REVERT: E 95 ASN cc_start: 0.8203 (m-40) cc_final: 0.7769 (m-40) REVERT: E 102 LEU cc_start: 0.7959 (tp) cc_final: 0.7664 (tp) REVERT: H 68 PHE cc_start: 0.7002 (m-80) cc_final: 0.6722 (m-80) REVERT: H 117 MET cc_start: 0.7184 (mtm) cc_final: 0.6801 (mpp) REVERT: H 181 HIS cc_start: 0.6230 (m-70) cc_final: 0.5847 (m-70) REVERT: L 18 ARG cc_start: 0.7346 (ttm170) cc_final: 0.7135 (ttm170) REVERT: L 29 ILE cc_start: 0.7441 (pt) cc_final: 0.7219 (tt) REVERT: L 139 PHE cc_start: 0.5220 (p90) cc_final: 0.4837 (p90) REVERT: L 180 THR cc_start: 0.7227 (m) cc_final: 0.6999 (t) REVERT: L 189 HIS cc_start: 0.7868 (m-70) cc_final: 0.7449 (m-70) REVERT: L 210 ASN cc_start: 0.7856 (t0) cc_final: 0.7636 (p0) REVERT: D 57 ARG cc_start: 0.7779 (ttt90) cc_final: 0.7118 (ttt180) REVERT: D 75 HIS cc_start: 0.6894 (m-70) cc_final: 0.6562 (m-70) REVERT: D 83 THR cc_start: 0.7616 (p) cc_final: 0.7040 (t) REVERT: D 119 GLU cc_start: 0.7612 (tt0) cc_final: 0.7293 (tt0) REVERT: D 127 TRP cc_start: 0.7951 (m-90) cc_final: 0.6641 (m-90) REVERT: D 150 ARG cc_start: 0.8122 (mmm160) cc_final: 0.7803 (mmm160) REVERT: D 184 HIS cc_start: 0.6355 (m-70) cc_final: 0.6014 (m-70) REVERT: D 186 SER cc_start: 0.8046 (p) cc_final: 0.7701 (m) REVERT: D 212 THR cc_start: 0.8306 (m) cc_final: 0.8058 (p) REVERT: D 326 LYS cc_start: 0.7835 (ptmm) cc_final: 0.6794 (ptpp) REVERT: F 34 GLN cc_start: 0.6968 (mt0) cc_final: 0.6700 (mp10) REVERT: F 41 THR cc_start: 0.7509 (m) cc_final: 0.7185 (m) REVERT: F 79 ASP cc_start: 0.7105 (m-30) cc_final: 0.6670 (m-30) REVERT: F 85 GLU cc_start: 0.7038 (tp30) cc_final: 0.6745 (tp30) REVERT: F 89 ILE cc_start: 0.8055 (mt) cc_final: 0.7494 (mt) REVERT: F 91 LEU cc_start: 0.7942 (mt) cc_final: 0.7713 (mt) REVERT: F 114 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6058 (mm-30) REVERT: F 115 MET cc_start: 0.5823 (tpp) cc_final: 0.5593 (tpp) REVERT: F 121 LYS cc_start: 0.8133 (tptp) cc_final: 0.7843 (tptp) REVERT: F 133 MET cc_start: 0.5388 (ptm) cc_final: 0.5148 (ptt) outliers start: 64 outliers final: 34 residues processed: 652 average time/residue: 0.1598 time to fit residues: 157.3295 Evaluate side-chains 619 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 582 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 81 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 243 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 106 ASN K 3 GLN K 6 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 GLN A 53 ASN A 152 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 160 GLN J 166 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN C 250 ASN ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS H 106 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN D 56 HIS F 42 GLN F 106 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.167939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.141688 restraints weight = 36492.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.147169 restraints weight = 17927.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.150782 restraints weight = 10287.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.153088 restraints weight = 6554.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.154630 restraints weight = 4569.062| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.157 21978 Z= 0.367 Angle : 0.838 11.628 29856 Z= 0.452 Chirality : 0.051 0.360 3309 Planarity : 0.006 0.064 3876 Dihedral : 5.772 59.646 3011 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.90 % Rotamer: Outliers : 4.16 % Allowed : 10.27 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.83 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.15), residues: 2754 helix: -0.78 (0.24), residues: 366 sheet: -0.89 (0.17), residues: 852 loop : -1.79 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 109 TYR 0.048 0.004 TYR E 141 PHE 0.033 0.003 PHE E 171 TRP 0.045 0.004 TRP G 36 HIS 0.017 0.003 HIS K 87 Details of bonding type rmsd covalent geometry : bond 0.00767 (21945) covalent geometry : angle 0.83474 (29790) SS BOND : bond 0.00682 ( 33) SS BOND : angle 1.86017 ( 66) hydrogen bonds : bond 0.06266 ( 616) hydrogen bonds : angle 7.03043 ( 1797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 630 time to evaluate : 0.726 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: I 3 GLN cc_start: 0.6257 (mp-120) cc_final: 0.5891 (mm-40) REVERT: I 22 CYS cc_start: 0.5327 (t) cc_final: 0.4926 (t) REVERT: I 68 PHE cc_start: 0.7692 (m-80) cc_final: 0.7377 (m-80) REVERT: I 83 MET cc_start: 0.5459 (mtp) cc_final: 0.4188 (mtp) REVERT: I 104 SER cc_start: 0.8558 (t) cc_final: 0.8284 (t) REVERT: I 110 VAL cc_start: 0.8147 (t) cc_final: 0.7916 (m) REVERT: I 117 MET cc_start: 0.7016 (mtm) cc_final: 0.6411 (mtt) REVERT: I 181 HIS cc_start: 0.5495 (m-70) cc_final: 0.5110 (m-70) REVERT: K 27 GLN cc_start: 0.6959 (pp30) cc_final: 0.6618 (pp30) REVERT: K 62 PHE cc_start: 0.7398 (t80) cc_final: 0.7159 (t80) REVERT: K 149 LYS cc_start: 0.7382 (tppt) cc_final: 0.6897 (tppt) REVERT: K 176 SER cc_start: 0.7677 (t) cc_final: 0.6857 (m) REVERT: K 210 ASN cc_start: 0.8367 (t0) cc_final: 0.7996 (p0) REVERT: A 53 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8370 (t0) REVERT: A 57 ARG cc_start: 0.7710 (ttt90) cc_final: 0.6883 (ttm-80) REVERT: A 75 HIS cc_start: 0.6616 (m-70) cc_final: 0.6088 (m-70) REVERT: A 82 GLU cc_start: 0.7748 (tp30) cc_final: 0.7398 (tp30) REVERT: A 119 GLU cc_start: 0.7386 (tt0) cc_final: 0.6516 (tt0) REVERT: A 121 ILE cc_start: 0.8116 (mp) cc_final: 0.7710 (mm) REVERT: A 123 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6212 (mm-30) REVERT: A 168 MET cc_start: 0.6289 (mmm) cc_final: 0.5653 (mmm) REVERT: A 184 HIS cc_start: 0.7033 (m-70) cc_final: 0.6104 (m170) REVERT: A 189 GLN cc_start: 0.7493 (mt0) cc_final: 0.7259 (mm-40) REVERT: A 261 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7419 (mtt90) REVERT: B 25 ARG cc_start: 0.7229 (tmt170) cc_final: 0.6661 (tmt170) REVERT: B 51 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7727 (ttmt) REVERT: B 79 ASP cc_start: 0.7286 (m-30) cc_final: 0.6971 (m-30) REVERT: B 85 GLU cc_start: 0.7515 (tp30) cc_final: 0.6916 (tp30) REVERT: B 89 ILE cc_start: 0.8416 (mt) cc_final: 0.7886 (mp) REVERT: B 94 TYR cc_start: 0.8605 (t80) cc_final: 0.7750 (t80) REVERT: B 115 MET cc_start: 0.5916 (tpp) cc_final: 0.5657 (tpp) REVERT: B 121 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7677 (tptp) REVERT: B 133 MET cc_start: 0.5784 (ptm) cc_final: 0.5414 (ptm) REVERT: G 3 GLN cc_start: 0.6583 (mp-120) cc_final: 0.6205 (mp10) REVERT: G 68 PHE cc_start: 0.7358 (m-80) cc_final: 0.7059 (m-80) REVERT: G 83 MET cc_start: 0.5175 (mtp) cc_final: 0.4228 (mtp) REVERT: J 5 THR cc_start: 0.7007 (OUTLIER) cc_final: 0.6786 (t) REVERT: J 18 ARG cc_start: 0.7297 (ttm170) cc_final: 0.7047 (ttm170) REVERT: J 65 SER cc_start: 0.8377 (t) cc_final: 0.7873 (m) REVERT: J 89 GLN cc_start: 0.6629 (pp30) cc_final: 0.6375 (pp30) REVERT: J 172 THR cc_start: 0.8450 (p) cc_final: 0.8201 (m) REVERT: J 179 LEU cc_start: 0.7807 (mt) cc_final: 0.7121 (mm) REVERT: J 189 HIS cc_start: 0.7887 (m-70) cc_final: 0.7669 (m-70) REVERT: C 50 LYS cc_start: 0.7298 (mttt) cc_final: 0.6675 (mtmm) REVERT: C 79 PHE cc_start: 0.7136 (m-80) cc_final: 0.6916 (m-10) REVERT: C 92 LYS cc_start: 0.8340 (pttp) cc_final: 0.8022 (pttp) REVERT: C 119 GLU cc_start: 0.7389 (tt0) cc_final: 0.6579 (tt0) REVERT: C 121 ILE cc_start: 0.8642 (mp) cc_final: 0.8348 (mm) REVERT: C 123 GLU cc_start: 0.6483 (mt-10) cc_final: 0.6195 (mt-10) REVERT: C 153 TRP cc_start: 0.7115 (t60) cc_final: 0.6813 (t-100) REVERT: C 167 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7830 (t) REVERT: C 184 HIS cc_start: 0.6761 (m-70) cc_final: 0.6133 (m170) REVERT: C 208 ARG cc_start: 0.7105 (mtt90) cc_final: 0.6542 (mtt90) REVERT: C 261 ARG cc_start: 0.7699 (mtt180) cc_final: 0.7463 (mtt90) REVERT: C 267 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6641 (tt) REVERT: C 281 CYS cc_start: 0.4472 (m) cc_final: 0.3376 (m) REVERT: C 290 ASN cc_start: 0.7077 (OUTLIER) cc_final: 0.5912 (m110) REVERT: E 25 ARG cc_start: 0.7169 (tmt170) cc_final: 0.6694 (tmt170) REVERT: E 42 GLN cc_start: 0.7664 (tp-100) cc_final: 0.7341 (tp-100) REVERT: E 78 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: E 79 ASP cc_start: 0.7457 (m-30) cc_final: 0.7119 (m-30) REVERT: E 85 GLU cc_start: 0.7397 (tp30) cc_final: 0.7007 (tp30) REVERT: E 88 LYS cc_start: 0.8496 (tttt) cc_final: 0.7945 (ttmt) REVERT: E 91 LEU cc_start: 0.7910 (mt) cc_final: 0.7304 (mt) REVERT: E 95 ASN cc_start: 0.8080 (m-40) cc_final: 0.7729 (m-40) REVERT: E 102 LEU cc_start: 0.8131 (tp) cc_final: 0.7889 (tp) REVERT: E 163 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.6462 (ttt-90) REVERT: H 3 GLN cc_start: 0.6240 (mp10) cc_final: 0.5819 (mp10) REVERT: H 20 LEU cc_start: 0.7635 (mt) cc_final: 0.7435 (mt) REVERT: H 65 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8464 (mmmm) REVERT: H 117 MET cc_start: 0.7444 (mtm) cc_final: 0.6280 (mpp) REVERT: H 181 HIS cc_start: 0.6079 (m-70) cc_final: 0.5733 (m-70) REVERT: L 6 GLN cc_start: 0.6335 (mp10) cc_final: 0.6085 (tt0) REVERT: L 29 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7842 (pt) REVERT: L 71 PHE cc_start: 0.7345 (m-80) cc_final: 0.7134 (m-80) REVERT: L 89 GLN cc_start: 0.5848 (tt0) cc_final: 0.5446 (tt0) REVERT: D 57 ARG cc_start: 0.7935 (ttt90) cc_final: 0.7312 (ttt90) REVERT: D 82 GLU cc_start: 0.7477 (tp30) cc_final: 0.7081 (tp30) REVERT: D 83 THR cc_start: 0.7759 (p) cc_final: 0.7428 (t) REVERT: D 141 ARG cc_start: 0.7527 (tpp-160) cc_final: 0.7214 (mmt180) REVERT: D 150 ARG cc_start: 0.7981 (mmm160) cc_final: 0.7610 (mmm160) REVERT: D 182 VAL cc_start: 0.5571 (OUTLIER) cc_final: 0.4933 (p) REVERT: D 184 HIS cc_start: 0.6828 (m-70) cc_final: 0.6408 (m-70) REVERT: D 224 ARG cc_start: 0.7925 (mpt180) cc_final: 0.7676 (mpt-90) REVERT: F 25 ARG cc_start: 0.6525 (tmt170) cc_final: 0.6290 (tmt170) REVERT: F 45 ILE cc_start: 0.8729 (mt) cc_final: 0.8344 (mt) REVERT: F 79 ASP cc_start: 0.7261 (m-30) cc_final: 0.6859 (m-30) REVERT: F 82 LYS cc_start: 0.8746 (mttp) cc_final: 0.8543 (mttp) REVERT: F 85 GLU cc_start: 0.7089 (tp30) cc_final: 0.6709 (tp30) REVERT: F 89 ILE cc_start: 0.8294 (mt) cc_final: 0.7973 (mt) REVERT: F 94 TYR cc_start: 0.8722 (t80) cc_final: 0.7631 (t80) REVERT: F 106 HIS cc_start: 0.6722 (t-90) cc_final: 0.6475 (t70) outliers start: 100 outliers final: 62 residues processed: 671 average time/residue: 0.1502 time to fit residues: 153.7809 Evaluate side-chains 662 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 591 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 158 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 226 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 198 optimal weight: 0.0470 chunk 4 optimal weight: 0.2980 chunk 205 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.0770 chunk 111 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 242 optimal weight: 0.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 3 GLN K 27 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN A 81 ASN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS B 42 GLN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS J 6 GLN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN D 56 HIS ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.174825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.149037 restraints weight = 36084.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.154580 restraints weight = 17658.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.158144 restraints weight = 10059.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.160422 restraints weight = 6365.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.161931 restraints weight = 4427.206| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21978 Z= 0.127 Angle : 0.615 11.269 29856 Z= 0.320 Chirality : 0.045 0.268 3309 Planarity : 0.004 0.054 3876 Dihedral : 4.894 54.006 3010 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.65 % Favored : 97.24 % Rotamer: Outliers : 3.33 % Allowed : 13.67 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 2754 helix: -0.20 (0.26), residues: 372 sheet: -0.76 (0.17), residues: 834 loop : -1.47 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 19 TYR 0.018 0.002 TYR E 22 PHE 0.028 0.002 PHE A 125 TRP 0.042 0.002 TRP B 14 HIS 0.006 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00279 (21945) covalent geometry : angle 0.61238 (29790) SS BOND : bond 0.00743 ( 33) SS BOND : angle 1.44909 ( 66) hydrogen bonds : bond 0.04111 ( 616) hydrogen bonds : angle 6.42235 ( 1797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 615 time to evaluate : 0.757 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: I 3 GLN cc_start: 0.6292 (mp-120) cc_final: 0.5896 (mm-40) REVERT: I 32 TYR cc_start: 0.6026 (m-80) cc_final: 0.5606 (m-80) REVERT: I 68 PHE cc_start: 0.7478 (m-80) cc_final: 0.7078 (m-80) REVERT: I 83 MET cc_start: 0.5003 (mtp) cc_final: 0.3495 (mtp) REVERT: I 104 SER cc_start: 0.8743 (t) cc_final: 0.8391 (t) REVERT: I 110 VAL cc_start: 0.8108 (t) cc_final: 0.7860 (m) REVERT: I 115 TYR cc_start: 0.5463 (m-80) cc_final: 0.4779 (m-80) REVERT: I 117 MET cc_start: 0.7008 (mtm) cc_final: 0.6482 (mtt) REVERT: I 181 HIS cc_start: 0.5885 (m-70) cc_final: 0.5407 (m-70) REVERT: K 62 PHE cc_start: 0.7218 (t80) cc_final: 0.7001 (t80) REVERT: K 147 GLN cc_start: 0.6124 (pp30) cc_final: 0.4653 (mp10) REVERT: K 148 TRP cc_start: 0.5902 (m100) cc_final: 0.5653 (m100) REVERT: K 176 SER cc_start: 0.7480 (t) cc_final: 0.6753 (m) REVERT: K 210 ASN cc_start: 0.8311 (t0) cc_final: 0.7939 (p0) REVERT: A 57 ARG cc_start: 0.7603 (ttt90) cc_final: 0.6704 (ttm-80) REVERT: A 75 HIS cc_start: 0.6541 (m-70) cc_final: 0.6105 (m-70) REVERT: A 119 GLU cc_start: 0.7327 (tt0) cc_final: 0.6577 (tt0) REVERT: A 121 ILE cc_start: 0.8256 (mp) cc_final: 0.7922 (mm) REVERT: A 123 GLU cc_start: 0.6488 (mm-30) cc_final: 0.6096 (mm-30) REVERT: A 172 ASP cc_start: 0.7438 (m-30) cc_final: 0.7053 (p0) REVERT: A 189 GLN cc_start: 0.7412 (mt0) cc_final: 0.7179 (mm-40) REVERT: A 241 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7164 (m-30) REVERT: A 261 ARG cc_start: 0.7434 (mtt180) cc_final: 0.7198 (mtt90) REVERT: B 25 ARG cc_start: 0.6938 (tmt170) cc_final: 0.6627 (tmt170) REVERT: B 51 LYS cc_start: 0.7703 (ttmt) cc_final: 0.7488 (ttmt) REVERT: B 79 ASP cc_start: 0.7045 (m-30) cc_final: 0.6839 (m-30) REVERT: B 85 GLU cc_start: 0.7313 (tp30) cc_final: 0.6982 (tp30) REVERT: B 94 TYR cc_start: 0.8266 (t80) cc_final: 0.7669 (t80) REVERT: B 121 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7585 (tptp) REVERT: B 133 MET cc_start: 0.5585 (ptm) cc_final: 0.5262 (ptm) REVERT: G 3 GLN cc_start: 0.6682 (mp-120) cc_final: 0.6280 (mp10) REVERT: G 68 PHE cc_start: 0.7131 (m-80) cc_final: 0.6887 (m-80) REVERT: G 83 MET cc_start: 0.4799 (OUTLIER) cc_final: 0.3934 (mtp) REVERT: J 18 ARG cc_start: 0.7187 (ttm170) cc_final: 0.6907 (ttm170) REVERT: J 20 THR cc_start: 0.8340 (m) cc_final: 0.8039 (t) REVERT: J 65 SER cc_start: 0.8269 (t) cc_final: 0.7816 (m) REVERT: J 71 PHE cc_start: 0.7081 (m-80) cc_final: 0.6858 (m-80) REVERT: J 189 HIS cc_start: 0.7862 (m-70) cc_final: 0.7637 (m-70) REVERT: C 71 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7614 (mt) REVERT: C 92 LYS cc_start: 0.8304 (pttp) cc_final: 0.7969 (pttp) REVERT: C 109 ARG cc_start: 0.7696 (ttp-170) cc_final: 0.7388 (mtp-110) REVERT: C 117 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7909 (m) REVERT: C 119 GLU cc_start: 0.7343 (tt0) cc_final: 0.6561 (tt0) REVERT: C 121 ILE cc_start: 0.8697 (mp) cc_final: 0.8492 (mm) REVERT: C 153 TRP cc_start: 0.6866 (t60) cc_final: 0.6600 (t-100) REVERT: C 161 TYR cc_start: 0.6665 (t80) cc_final: 0.6301 (t80) REVERT: C 167 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7777 (t) REVERT: C 189 GLN cc_start: 0.7277 (mt0) cc_final: 0.7059 (mm-40) REVERT: C 197 GLN cc_start: 0.6552 (pp30) cc_final: 0.5806 (pp30) REVERT: C 208 ARG cc_start: 0.7074 (mtt90) cc_final: 0.6503 (mtt90) REVERT: C 261 ARG cc_start: 0.7397 (mtt180) cc_final: 0.7079 (mtt90) REVERT: C 290 ASN cc_start: 0.7030 (OUTLIER) cc_final: 0.6718 (p0) REVERT: E 25 ARG cc_start: 0.7002 (tmt170) cc_final: 0.6723 (tmt170) REVERT: E 78 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7234 (pt0) REVERT: E 79 ASP cc_start: 0.6997 (m-30) cc_final: 0.6620 (m-30) REVERT: E 85 GLU cc_start: 0.7030 (tp30) cc_final: 0.6781 (tp30) REVERT: E 88 LYS cc_start: 0.8362 (tttt) cc_final: 0.8051 (ttmt) REVERT: E 91 LEU cc_start: 0.7683 (mt) cc_final: 0.7208 (mt) REVERT: E 95 ASN cc_start: 0.7905 (m-40) cc_final: 0.7364 (m-40) REVERT: E 102 LEU cc_start: 0.7913 (tp) cc_final: 0.7656 (tp) REVERT: E 114 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5380 (mm-30) REVERT: E 117 LYS cc_start: 0.7867 (mttp) cc_final: 0.7656 (mttp) REVERT: E 133 MET cc_start: 0.5658 (ptm) cc_final: 0.5315 (ppp) REVERT: E 135 ASN cc_start: 0.5586 (p0) cc_final: 0.5036 (p0) REVERT: E 163 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.6413 (ttt-90) REVERT: H 3 GLN cc_start: 0.6442 (mp10) cc_final: 0.6019 (mp10) REVERT: H 64 VAL cc_start: 0.5584 (t) cc_final: 0.4451 (m) REVERT: H 65 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8451 (mmmt) REVERT: H 72 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7162 (ttt180) REVERT: H 117 MET cc_start: 0.7166 (mtm) cc_final: 0.6205 (mpp) REVERT: H 181 HIS cc_start: 0.6001 (m-70) cc_final: 0.5664 (m-70) REVERT: L 74 THR cc_start: 0.7556 (m) cc_final: 0.7120 (p) REVERT: L 89 GLN cc_start: 0.5479 (tt0) cc_final: 0.5066 (tt0) REVERT: D 57 ARG cc_start: 0.7863 (ttt90) cc_final: 0.7237 (ttt90) REVERT: D 79 PHE cc_start: 0.6860 (m-10) cc_final: 0.6623 (m-10) REVERT: D 82 GLU cc_start: 0.7317 (tp30) cc_final: 0.7036 (tp30) REVERT: D 110 SER cc_start: 0.6347 (OUTLIER) cc_final: 0.6026 (t) REVERT: D 123 GLU cc_start: 0.5579 (mt-10) cc_final: 0.4914 (tt0) REVERT: D 125 PHE cc_start: 0.6548 (m-80) cc_final: 0.6304 (m-80) REVERT: D 127 TRP cc_start: 0.7860 (m-10) cc_final: 0.6779 (m-90) REVERT: D 150 ARG cc_start: 0.7839 (mmm160) cc_final: 0.7468 (mmm160) REVERT: D 168 MET cc_start: 0.6684 (mmm) cc_final: 0.5677 (mmm) REVERT: D 184 HIS cc_start: 0.6702 (m-70) cc_final: 0.6192 (m-70) REVERT: D 224 ARG cc_start: 0.7868 (mpt180) cc_final: 0.7617 (mpt-90) REVERT: D 260 MET cc_start: 0.7249 (mmm) cc_final: 0.7005 (mmm) REVERT: F 41 THR cc_start: 0.7511 (m) cc_final: 0.7188 (m) REVERT: F 79 ASP cc_start: 0.6979 (m-30) cc_final: 0.6625 (m-30) REVERT: F 85 GLU cc_start: 0.6827 (tp30) cc_final: 0.6413 (tp30) REVERT: F 89 ILE cc_start: 0.8093 (mt) cc_final: 0.7785 (mt) REVERT: F 94 TYR cc_start: 0.8562 (t80) cc_final: 0.7733 (t80) REVERT: F 97 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6929 (mt-10) REVERT: F 121 LYS cc_start: 0.8074 (tptp) cc_final: 0.7757 (tptp) outliers start: 80 outliers final: 48 residues processed: 651 average time/residue: 0.1697 time to fit residues: 166.6512 Evaluate side-chains 653 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 595 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 105 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 216 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 204 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 206 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 27 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 GLN C 81 ASN C 132 GLN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.170997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.144682 restraints weight = 35942.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.150208 restraints weight = 17704.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.153776 restraints weight = 10178.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.156069 restraints weight = 6504.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.157580 restraints weight = 4554.780| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 21978 Z= 0.190 Angle : 0.647 11.244 29856 Z= 0.339 Chirality : 0.046 0.416 3309 Planarity : 0.004 0.056 3876 Dihedral : 5.048 54.812 3010 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.75 % Rotamer: Outliers : 3.66 % Allowed : 15.17 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.15), residues: 2754 helix: -0.03 (0.26), residues: 372 sheet: -0.64 (0.17), residues: 810 loop : -1.51 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 19 TYR 0.017 0.002 TYR E 141 PHE 0.019 0.002 PHE C 125 TRP 0.040 0.002 TRP J 35 HIS 0.013 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00418 (21945) covalent geometry : angle 0.64044 (29790) SS BOND : bond 0.00460 ( 33) SS BOND : angle 2.01692 ( 66) hydrogen bonds : bond 0.04477 ( 616) hydrogen bonds : angle 6.36187 ( 1797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 616 time to evaluate : 0.791 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: I 3 GLN cc_start: 0.6278 (mp-120) cc_final: 0.5764 (mp-120) REVERT: I 22 CYS cc_start: 0.5614 (t) cc_final: 0.5171 (t) REVERT: I 51 ILE cc_start: 0.6422 (OUTLIER) cc_final: 0.6135 (tp) REVERT: I 68 PHE cc_start: 0.7520 (m-80) cc_final: 0.7030 (m-80) REVERT: I 70 ILE cc_start: 0.8252 (pt) cc_final: 0.7750 (mp) REVERT: I 83 MET cc_start: 0.5237 (mtp) cc_final: 0.3536 (mtp) REVERT: I 104 SER cc_start: 0.8790 (t) cc_final: 0.8422 (t) REVERT: I 108 TYR cc_start: 0.5993 (m-80) cc_final: 0.5751 (m-80) REVERT: I 110 VAL cc_start: 0.8175 (t) cc_final: 0.7928 (m) REVERT: I 117 MET cc_start: 0.7065 (mtm) cc_final: 0.6483 (mtt) REVERT: I 171 TRP cc_start: 0.6626 (m100) cc_final: 0.6222 (m100) REVERT: I 181 HIS cc_start: 0.5926 (m-70) cc_final: 0.5416 (m-70) REVERT: K 29 ILE cc_start: 0.7958 (tt) cc_final: 0.7490 (mp) REVERT: K 62 PHE cc_start: 0.7310 (t80) cc_final: 0.7046 (t80) REVERT: K 74 THR cc_start: 0.7773 (m) cc_final: 0.7098 (p) REVERT: K 85 THR cc_start: 0.5257 (m) cc_final: 0.4884 (m) REVERT: K 147 GLN cc_start: 0.6246 (pp30) cc_final: 0.4884 (mp10) REVERT: K 176 SER cc_start: 0.7517 (t) cc_final: 0.6699 (m) REVERT: K 210 ASN cc_start: 0.8354 (t0) cc_final: 0.7970 (p0) REVERT: A 57 ARG cc_start: 0.7597 (ttt90) cc_final: 0.6778 (ttm-80) REVERT: A 75 HIS cc_start: 0.6637 (m-70) cc_final: 0.6191 (m-70) REVERT: A 119 GLU cc_start: 0.7451 (tt0) cc_final: 0.6657 (tt0) REVERT: A 121 ILE cc_start: 0.8201 (mp) cc_final: 0.7849 (mm) REVERT: A 123 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6209 (mm-30) REVERT: A 125 PHE cc_start: 0.6315 (m-80) cc_final: 0.6077 (m-80) REVERT: A 189 GLN cc_start: 0.7480 (mt0) cc_final: 0.7245 (mm-40) REVERT: A 233 TYR cc_start: 0.6104 (m-80) cc_final: 0.5876 (m-80) REVERT: A 241 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7244 (m-30) REVERT: A 268 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7547 (ttm) REVERT: B 51 LYS cc_start: 0.7917 (ttmt) cc_final: 0.7710 (ttmt) REVERT: B 79 ASP cc_start: 0.7160 (m-30) cc_final: 0.6894 (m-30) REVERT: B 85 GLU cc_start: 0.7434 (tp30) cc_final: 0.6990 (tp30) REVERT: B 89 ILE cc_start: 0.8267 (mt) cc_final: 0.7768 (mt) REVERT: B 94 TYR cc_start: 0.8328 (t80) cc_final: 0.7588 (t80) REVERT: B 121 LYS cc_start: 0.8119 (ttpt) cc_final: 0.7679 (tptp) REVERT: B 133 MET cc_start: 0.5516 (ptm) cc_final: 0.5182 (ptm) REVERT: G 3 GLN cc_start: 0.6679 (mp-120) cc_final: 0.6259 (mp10) REVERT: G 68 PHE cc_start: 0.7270 (m-80) cc_final: 0.6867 (m-80) REVERT: G 83 MET cc_start: 0.5057 (OUTLIER) cc_final: 0.4116 (mtp) REVERT: J 6 GLN cc_start: 0.5937 (mp10) cc_final: 0.5574 (mp10) REVERT: J 11 VAL cc_start: 0.8638 (p) cc_final: 0.8413 (m) REVERT: J 18 ARG cc_start: 0.7298 (ttm170) cc_final: 0.6983 (ttm170) REVERT: J 46 LEU cc_start: 0.4813 (tp) cc_final: 0.4221 (tp) REVERT: J 65 SER cc_start: 0.8306 (t) cc_final: 0.7875 (m) REVERT: J 89 GLN cc_start: 0.6600 (pp30) cc_final: 0.6326 (pp30) REVERT: J 189 HIS cc_start: 0.7941 (m-70) cc_final: 0.7736 (m-70) REVERT: C 71 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7746 (mt) REVERT: C 92 LYS cc_start: 0.8342 (pttp) cc_final: 0.8000 (pttp) REVERT: C 100 TYR cc_start: 0.7457 (p90) cc_final: 0.7134 (p90) REVERT: C 109 ARG cc_start: 0.7691 (ttp-170) cc_final: 0.7321 (mtp-110) REVERT: C 117 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7928 (m) REVERT: C 119 GLU cc_start: 0.7413 (tt0) cc_final: 0.6606 (tt0) REVERT: C 121 ILE cc_start: 0.8630 (mp) cc_final: 0.8394 (mm) REVERT: C 153 TRP cc_start: 0.7041 (t60) cc_final: 0.6757 (t-100) REVERT: C 161 TYR cc_start: 0.6838 (t80) cc_final: 0.6599 (t80) REVERT: C 189 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.7134 (mm-40) REVERT: C 197 GLN cc_start: 0.6867 (pp30) cc_final: 0.6050 (pp30) REVERT: C 208 ARG cc_start: 0.7102 (mtt90) cc_final: 0.6522 (mtt90) REVERT: C 261 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7193 (mtt90) REVERT: E 42 GLN cc_start: 0.7256 (tp40) cc_final: 0.6987 (tp-100) REVERT: E 78 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7257 (pt0) REVERT: E 79 ASP cc_start: 0.7136 (m-30) cc_final: 0.6827 (m-30) REVERT: E 85 GLU cc_start: 0.7333 (tp30) cc_final: 0.6972 (tp30) REVERT: E 88 LYS cc_start: 0.8489 (tttt) cc_final: 0.8106 (ttmt) REVERT: E 91 LEU cc_start: 0.7660 (mt) cc_final: 0.7249 (mt) REVERT: E 95 ASN cc_start: 0.7967 (m-40) cc_final: 0.7403 (m-40) REVERT: E 102 LEU cc_start: 0.8083 (tp) cc_final: 0.7815 (tp) REVERT: E 135 ASN cc_start: 0.5902 (p0) cc_final: 0.5521 (p0) REVERT: E 163 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.6375 (ttt-90) REVERT: H 3 GLN cc_start: 0.6349 (mp10) cc_final: 0.5928 (mp10) REVERT: H 65 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8568 (mmmt) REVERT: H 72 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7436 (ttt180) REVERT: H 83 MET cc_start: 0.5318 (OUTLIER) cc_final: 0.4913 (mtp) REVERT: H 112 TYR cc_start: 0.5414 (m-10) cc_final: 0.5154 (m-10) REVERT: H 117 MET cc_start: 0.6960 (mtm) cc_final: 0.5879 (mpp) REVERT: H 181 HIS cc_start: 0.6031 (m-70) cc_final: 0.5697 (m-70) REVERT: L 74 THR cc_start: 0.7617 (m) cc_final: 0.7179 (p) REVERT: L 89 GLN cc_start: 0.5711 (tt0) cc_final: 0.5134 (tt0) REVERT: L 148 TRP cc_start: 0.6382 (m100) cc_final: 0.6017 (m100) REVERT: D 57 ARG cc_start: 0.7880 (ttt90) cc_final: 0.7246 (ttt90) REVERT: D 71 LEU cc_start: 0.7613 (mm) cc_final: 0.7242 (mm) REVERT: D 79 PHE cc_start: 0.7012 (m-10) cc_final: 0.6773 (m-10) REVERT: D 82 GLU cc_start: 0.7468 (tp30) cc_final: 0.7202 (tp30) REVERT: D 123 GLU cc_start: 0.6175 (mt-10) cc_final: 0.5957 (mt-10) REVERT: D 125 PHE cc_start: 0.6901 (m-80) cc_final: 0.6632 (m-80) REVERT: D 127 TRP cc_start: 0.7911 (m-10) cc_final: 0.7235 (m-90) REVERT: D 150 ARG cc_start: 0.7848 (mmm160) cc_final: 0.7640 (mmm160) REVERT: D 184 HIS cc_start: 0.6822 (m-70) cc_final: 0.6328 (m-70) REVERT: D 224 ARG cc_start: 0.7869 (mpt180) cc_final: 0.7607 (mpt-90) REVERT: D 260 MET cc_start: 0.7352 (mmm) cc_final: 0.7031 (mmm) REVERT: D 281 CYS cc_start: 0.4732 (OUTLIER) cc_final: 0.4438 (p) REVERT: F 41 THR cc_start: 0.7599 (m) cc_final: 0.7250 (m) REVERT: F 79 ASP cc_start: 0.7122 (m-30) cc_final: 0.6755 (m-30) REVERT: F 85 GLU cc_start: 0.6871 (tp30) cc_final: 0.6570 (tp30) REVERT: F 89 ILE cc_start: 0.8177 (mt) cc_final: 0.7886 (mt) REVERT: F 97 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7138 (mt-10) outliers start: 88 outliers final: 62 residues processed: 657 average time/residue: 0.1655 time to fit residues: 164.3869 Evaluate side-chains 677 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 603 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 281 CYS Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 158 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 34 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 87 optimal weight: 0.1980 chunk 186 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 227 optimal weight: 0.4980 chunk 125 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN A 81 ASN B 42 GLN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 GLN C 81 ASN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS D 132 GLN F 106 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.171644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.145095 restraints weight = 35974.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.150611 restraints weight = 17750.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.154248 restraints weight = 10212.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.156584 restraints weight = 6512.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.158128 restraints weight = 4554.059| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 21978 Z= 0.160 Angle : 0.642 10.122 29856 Z= 0.333 Chirality : 0.045 0.286 3309 Planarity : 0.005 0.055 3876 Dihedral : 5.019 56.290 3010 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 3.28 % Allowed : 16.38 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 2754 helix: 0.03 (0.26), residues: 372 sheet: -0.52 (0.17), residues: 810 loop : -1.38 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 103 TYR 0.020 0.002 TYR F 83 PHE 0.019 0.002 PHE H 68 TRP 0.042 0.002 TRP B 14 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00359 (21945) covalent geometry : angle 0.63504 (29790) SS BOND : bond 0.00481 ( 33) SS BOND : angle 2.11662 ( 66) hydrogen bonds : bond 0.04230 ( 616) hydrogen bonds : angle 6.28941 ( 1797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 608 time to evaluate : 0.755 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: I 3 GLN cc_start: 0.6270 (mp-120) cc_final: 0.5740 (mp-120) REVERT: I 51 ILE cc_start: 0.6165 (OUTLIER) cc_final: 0.5786 (tp) REVERT: I 68 PHE cc_start: 0.7506 (m-80) cc_final: 0.7000 (m-80) REVERT: I 83 MET cc_start: 0.5285 (mtp) cc_final: 0.3665 (mtp) REVERT: I 104 SER cc_start: 0.8808 (t) cc_final: 0.8434 (t) REVERT: I 108 TYR cc_start: 0.6022 (m-80) cc_final: 0.5761 (m-80) REVERT: I 117 MET cc_start: 0.7084 (mtm) cc_final: 0.6592 (mtt) REVERT: I 171 TRP cc_start: 0.6562 (m100) cc_final: 0.6282 (m100) REVERT: I 181 HIS cc_start: 0.5907 (m-70) cc_final: 0.5398 (m-70) REVERT: K 62 PHE cc_start: 0.7312 (t80) cc_final: 0.7040 (t80) REVERT: K 74 THR cc_start: 0.7890 (m) cc_final: 0.7138 (p) REVERT: K 85 THR cc_start: 0.5103 (m) cc_final: 0.4735 (m) REVERT: K 147 GLN cc_start: 0.6311 (pp30) cc_final: 0.4771 (mp10) REVERT: A 57 ARG cc_start: 0.7563 (ttt90) cc_final: 0.6783 (ttm-80) REVERT: A 75 HIS cc_start: 0.6618 (m-70) cc_final: 0.6251 (m-70) REVERT: A 119 GLU cc_start: 0.7434 (tt0) cc_final: 0.6552 (tt0) REVERT: A 121 ILE cc_start: 0.8256 (mp) cc_final: 0.7805 (mm) REVERT: A 123 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6252 (mm-30) REVERT: A 125 PHE cc_start: 0.6417 (m-80) cc_final: 0.6124 (m-80) REVERT: A 189 GLN cc_start: 0.7480 (mt0) cc_final: 0.7253 (mm-40) REVERT: A 233 TYR cc_start: 0.6146 (m-80) cc_final: 0.5843 (m-80) REVERT: A 241 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: A 261 ARG cc_start: 0.7430 (mtt90) cc_final: 0.7084 (mtt90) REVERT: A 268 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7554 (ttm) REVERT: A 275 ASP cc_start: 0.6875 (t70) cc_final: 0.6536 (t70) REVERT: B 14 TRP cc_start: 0.5896 (m100) cc_final: 0.5578 (m100) REVERT: B 65 GLN cc_start: 0.7491 (mm-40) cc_final: 0.7230 (mm-40) REVERT: B 79 ASP cc_start: 0.7131 (m-30) cc_final: 0.6839 (m-30) REVERT: B 85 GLU cc_start: 0.7188 (tp30) cc_final: 0.6760 (tp30) REVERT: B 89 ILE cc_start: 0.8228 (mt) cc_final: 0.7834 (mt) REVERT: B 94 TYR cc_start: 0.8292 (t80) cc_final: 0.7626 (t80) REVERT: B 121 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7634 (tptp) REVERT: B 133 MET cc_start: 0.5458 (ptm) cc_final: 0.5104 (ptm) REVERT: G 3 GLN cc_start: 0.6669 (mp-120) cc_final: 0.6231 (mp10) REVERT: G 68 PHE cc_start: 0.7254 (m-80) cc_final: 0.6828 (m-80) REVERT: G 83 MET cc_start: 0.4993 (OUTLIER) cc_final: 0.3998 (mtp) REVERT: G 160 LYS cc_start: 0.7205 (tppt) cc_final: 0.6949 (tppt) REVERT: J 11 VAL cc_start: 0.8640 (p) cc_final: 0.8421 (m) REVERT: J 18 ARG cc_start: 0.7133 (ttm170) cc_final: 0.6856 (ttm170) REVERT: J 46 LEU cc_start: 0.4793 (tp) cc_final: 0.4306 (tp) REVERT: J 65 SER cc_start: 0.8279 (t) cc_final: 0.7801 (m) REVERT: C 71 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7747 (mt) REVERT: C 92 LYS cc_start: 0.8318 (pttp) cc_final: 0.7987 (pttp) REVERT: C 109 ARG cc_start: 0.7632 (ttp-170) cc_final: 0.7323 (mtp-110) REVERT: C 117 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7906 (m) REVERT: C 119 GLU cc_start: 0.7397 (tt0) cc_final: 0.6597 (tt0) REVERT: C 121 ILE cc_start: 0.8624 (mp) cc_final: 0.8376 (mm) REVERT: C 123 GLU cc_start: 0.6232 (mt-10) cc_final: 0.5936 (mt-10) REVERT: C 153 TRP cc_start: 0.7017 (t60) cc_final: 0.6675 (t-100) REVERT: C 161 TYR cc_start: 0.6881 (t80) cc_final: 0.6637 (t80) REVERT: C 189 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.7143 (mm-40) REVERT: C 197 GLN cc_start: 0.6932 (pp30) cc_final: 0.6035 (pp30) REVERT: C 208 ARG cc_start: 0.7143 (mtt90) cc_final: 0.6548 (mtt90) REVERT: C 261 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7176 (mtt90) REVERT: E 42 GLN cc_start: 0.7402 (tp40) cc_final: 0.7179 (tp-100) REVERT: E 78 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7209 (pt0) REVERT: E 79 ASP cc_start: 0.7123 (m-30) cc_final: 0.6737 (m-30) REVERT: E 85 GLU cc_start: 0.7164 (tp30) cc_final: 0.6874 (tp30) REVERT: E 88 LYS cc_start: 0.8478 (tttt) cc_final: 0.8083 (ttmt) REVERT: E 91 LEU cc_start: 0.7646 (mt) cc_final: 0.7246 (mt) REVERT: E 95 ASN cc_start: 0.7949 (m-40) cc_final: 0.7368 (m-40) REVERT: E 102 LEU cc_start: 0.8048 (tp) cc_final: 0.7832 (tp) REVERT: H 3 GLN cc_start: 0.6328 (mp10) cc_final: 0.5869 (mp10) REVERT: H 65 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8505 (mmmt) REVERT: H 72 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7540 (ttt180) REVERT: H 117 MET cc_start: 0.6824 (mtm) cc_final: 0.6049 (mpp) REVERT: H 181 HIS cc_start: 0.6069 (m-70) cc_final: 0.5731 (m-70) REVERT: L 74 THR cc_start: 0.7597 (m) cc_final: 0.7148 (p) REVERT: L 79 GLN cc_start: 0.7416 (mm-40) cc_final: 0.6886 (mm-40) REVERT: L 89 GLN cc_start: 0.5685 (tt0) cc_final: 0.5187 (tt0) REVERT: L 148 TRP cc_start: 0.6363 (m100) cc_final: 0.5954 (m100) REVERT: D 50 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6682 (mtmm) REVERT: D 57 ARG cc_start: 0.7877 (ttt90) cc_final: 0.7255 (ttt90) REVERT: D 67 ILE cc_start: 0.7773 (mm) cc_final: 0.7173 (tp) REVERT: D 71 LEU cc_start: 0.7606 (mm) cc_final: 0.7237 (mm) REVERT: D 79 PHE cc_start: 0.6969 (m-10) cc_final: 0.6642 (m-80) REVERT: D 82 GLU cc_start: 0.7448 (tp30) cc_final: 0.7198 (tp30) REVERT: D 110 SER cc_start: 0.6460 (OUTLIER) cc_final: 0.6072 (t) REVERT: D 123 GLU cc_start: 0.5994 (mt-10) cc_final: 0.5781 (mt-10) REVERT: D 125 PHE cc_start: 0.6869 (m-80) cc_final: 0.6650 (m-80) REVERT: D 127 TRP cc_start: 0.7969 (m-10) cc_final: 0.6638 (m-90) REVERT: D 141 ARG cc_start: 0.7494 (tpp-160) cc_final: 0.7172 (mmt180) REVERT: D 150 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7690 (mmm160) REVERT: D 184 HIS cc_start: 0.6812 (m-70) cc_final: 0.6309 (m-70) REVERT: D 224 ARG cc_start: 0.7864 (mpt180) cc_final: 0.7601 (mpt-90) REVERT: D 260 MET cc_start: 0.7317 (mmm) cc_final: 0.6943 (mmm) REVERT: F 79 ASP cc_start: 0.7077 (m-30) cc_final: 0.6681 (m-30) REVERT: F 82 LYS cc_start: 0.8606 (mttp) cc_final: 0.8394 (mttp) REVERT: F 85 GLU cc_start: 0.6870 (tp30) cc_final: 0.6557 (tp30) REVERT: F 89 ILE cc_start: 0.8154 (mt) cc_final: 0.7894 (mt) outliers start: 79 outliers final: 59 residues processed: 641 average time/residue: 0.1666 time to fit residues: 160.9348 Evaluate side-chains 660 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 590 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 158 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 79 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 177 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 27 GLN ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN A 81 ASN B 42 GLN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS F 106 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.169419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.142293 restraints weight = 36047.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.147899 restraints weight = 17883.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.151560 restraints weight = 10332.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.153951 restraints weight = 6638.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.155515 restraints weight = 4654.251| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 21978 Z= 0.207 Angle : 0.683 12.213 29856 Z= 0.357 Chirality : 0.046 0.319 3309 Planarity : 0.005 0.058 3876 Dihedral : 5.242 54.557 3010 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.16 % Favored : 94.73 % Rotamer: Outliers : 4.03 % Allowed : 16.25 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.15), residues: 2754 helix: 0.13 (0.26), residues: 366 sheet: -0.52 (0.17), residues: 810 loop : -1.44 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 103 TYR 0.024 0.002 TYR F 83 PHE 0.031 0.002 PHE I 29 TRP 0.052 0.003 TRP H 36 HIS 0.008 0.001 HIS J 87 Details of bonding type rmsd covalent geometry : bond 0.00451 (21945) covalent geometry : angle 0.67524 (29790) SS BOND : bond 0.00506 ( 33) SS BOND : angle 2.24667 ( 66) hydrogen bonds : bond 0.04571 ( 616) hydrogen bonds : angle 6.36077 ( 1797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 600 time to evaluate : 0.767 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: I 3 GLN cc_start: 0.6275 (mp-120) cc_final: 0.5982 (mp-120) REVERT: I 22 CYS cc_start: 0.5731 (t) cc_final: 0.5254 (t) REVERT: I 68 PHE cc_start: 0.7534 (m-80) cc_final: 0.6991 (m-80) REVERT: I 83 MET cc_start: 0.5384 (mtp) cc_final: 0.3650 (mtp) REVERT: I 104 SER cc_start: 0.8823 (t) cc_final: 0.8376 (p) REVERT: I 108 TYR cc_start: 0.6083 (m-80) cc_final: 0.5799 (m-80) REVERT: I 117 MET cc_start: 0.7201 (mtm) cc_final: 0.6229 (mtt) REVERT: I 171 TRP cc_start: 0.6721 (m100) cc_final: 0.6257 (m100) REVERT: I 181 HIS cc_start: 0.5944 (m-70) cc_final: 0.5433 (m-70) REVERT: K 62 PHE cc_start: 0.7360 (t80) cc_final: 0.7033 (t80) REVERT: K 74 THR cc_start: 0.7926 (m) cc_final: 0.7185 (p) REVERT: K 85 THR cc_start: 0.5193 (m) cc_final: 0.4856 (m) REVERT: A 57 ARG cc_start: 0.7542 (ttt90) cc_final: 0.6695 (ttt90) REVERT: A 75 HIS cc_start: 0.6682 (m-70) cc_final: 0.6291 (m-70) REVERT: A 117 THR cc_start: 0.8673 (t) cc_final: 0.8179 (m) REVERT: A 119 GLU cc_start: 0.7444 (tt0) cc_final: 0.6580 (tt0) REVERT: A 121 ILE cc_start: 0.8286 (mp) cc_final: 0.7872 (mm) REVERT: A 123 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6431 (mm-30) REVERT: A 125 PHE cc_start: 0.6520 (m-80) cc_final: 0.6267 (m-10) REVERT: A 189 GLN cc_start: 0.7558 (mt0) cc_final: 0.7338 (mm-40) REVERT: A 233 TYR cc_start: 0.6476 (m-80) cc_final: 0.6060 (m-80) REVERT: A 241 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7315 (m-30) REVERT: A 261 ARG cc_start: 0.7546 (mtt90) cc_final: 0.7058 (mtt90) REVERT: A 268 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7638 (ttt) REVERT: A 275 ASP cc_start: 0.6793 (t70) cc_final: 0.6448 (t70) REVERT: B 14 TRP cc_start: 0.6094 (m100) cc_final: 0.5865 (m100) REVERT: B 79 ASP cc_start: 0.7219 (m-30) cc_final: 0.6867 (m-30) REVERT: B 85 GLU cc_start: 0.7224 (tp30) cc_final: 0.6917 (tp30) REVERT: B 89 ILE cc_start: 0.8294 (mt) cc_final: 0.8010 (mt) REVERT: B 94 TYR cc_start: 0.8333 (t80) cc_final: 0.7712 (t80) REVERT: B 117 LYS cc_start: 0.7953 (mttp) cc_final: 0.7607 (mttm) REVERT: B 121 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7682 (tptp) REVERT: G 3 GLN cc_start: 0.6659 (mp-120) cc_final: 0.6163 (mp10) REVERT: G 68 PHE cc_start: 0.7328 (m-80) cc_final: 0.6863 (m-80) REVERT: G 83 MET cc_start: 0.5061 (OUTLIER) cc_final: 0.4001 (mtp) REVERT: G 160 LYS cc_start: 0.7180 (tppt) cc_final: 0.6886 (tppt) REVERT: J 6 GLN cc_start: 0.6315 (mp10) cc_final: 0.6079 (mp10) REVERT: J 11 VAL cc_start: 0.8649 (p) cc_final: 0.8403 (m) REVERT: J 18 ARG cc_start: 0.7173 (ttm170) cc_final: 0.6915 (ttm170) REVERT: J 46 LEU cc_start: 0.5098 (tp) cc_final: 0.4618 (tp) REVERT: J 65 SER cc_start: 0.8235 (t) cc_final: 0.7791 (m) REVERT: J 148 TRP cc_start: 0.5487 (m100) cc_final: 0.4993 (m100) REVERT: C 71 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7797 (mt) REVERT: C 119 GLU cc_start: 0.7471 (tt0) cc_final: 0.7035 (tt0) REVERT: C 132 GLN cc_start: 0.7709 (tt0) cc_final: 0.7023 (tm-30) REVERT: C 153 TRP cc_start: 0.7104 (t60) cc_final: 0.6752 (t-100) REVERT: C 161 TYR cc_start: 0.7023 (t80) cc_final: 0.6799 (t80) REVERT: C 189 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7203 (mm-40) REVERT: C 197 GLN cc_start: 0.7155 (pp30) cc_final: 0.6250 (pp30) REVERT: C 208 ARG cc_start: 0.7132 (mtt90) cc_final: 0.6542 (mtt90) REVERT: E 42 GLN cc_start: 0.7597 (tp40) cc_final: 0.7338 (tp-100) REVERT: E 78 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7422 (pt0) REVERT: E 79 ASP cc_start: 0.7287 (m-30) cc_final: 0.6962 (m-30) REVERT: E 85 GLU cc_start: 0.7355 (tp30) cc_final: 0.7033 (tp30) REVERT: E 91 LEU cc_start: 0.7680 (mt) cc_final: 0.7238 (mt) REVERT: E 95 ASN cc_start: 0.8008 (m-40) cc_final: 0.7458 (m-40) REVERT: H 3 GLN cc_start: 0.6360 (mp10) cc_final: 0.5830 (mp10) REVERT: H 65 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8354 (tppp) REVERT: H 72 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7629 (ttt180) REVERT: H 117 MET cc_start: 0.6955 (mtm) cc_final: 0.5821 (mpp) REVERT: H 181 HIS cc_start: 0.6094 (m-70) cc_final: 0.5756 (m-70) REVERT: L 74 THR cc_start: 0.7815 (m) cc_final: 0.7390 (p) REVERT: L 79 GLN cc_start: 0.7289 (mm-40) cc_final: 0.6723 (mm-40) REVERT: L 89 GLN cc_start: 0.5729 (tt0) cc_final: 0.5140 (tt0) REVERT: L 148 TRP cc_start: 0.6442 (m100) cc_final: 0.6019 (m100) REVERT: L 176 SER cc_start: 0.6913 (t) cc_final: 0.6462 (p) REVERT: D 57 ARG cc_start: 0.7890 (ttt90) cc_final: 0.7396 (ttt90) REVERT: D 67 ILE cc_start: 0.7809 (mm) cc_final: 0.7207 (tp) REVERT: D 71 LEU cc_start: 0.7624 (mm) cc_final: 0.7276 (mm) REVERT: D 127 TRP cc_start: 0.8115 (m-10) cc_final: 0.6727 (m-90) REVERT: D 131 THR cc_start: 0.7688 (m) cc_final: 0.7316 (p) REVERT: D 141 ARG cc_start: 0.7506 (tpp-160) cc_final: 0.7180 (mmt180) REVERT: D 150 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7492 (mmm160) REVERT: D 184 HIS cc_start: 0.6794 (m-70) cc_final: 0.6244 (m170) REVERT: D 224 ARG cc_start: 0.7888 (mpt180) cc_final: 0.7608 (mpt-90) REVERT: D 281 CYS cc_start: 0.5125 (OUTLIER) cc_final: 0.4800 (p) REVERT: D 307 LYS cc_start: 0.5677 (mmmt) cc_final: 0.5305 (mmmt) REVERT: D 326 LYS cc_start: 0.7929 (ptmm) cc_final: 0.7688 (pptt) REVERT: F 79 ASP cc_start: 0.7188 (m-30) cc_final: 0.6784 (m-30) REVERT: F 85 GLU cc_start: 0.6879 (tp30) cc_final: 0.6593 (tp30) REVERT: F 89 ILE cc_start: 0.8187 (mt) cc_final: 0.7866 (mt) outliers start: 97 outliers final: 66 residues processed: 641 average time/residue: 0.1556 time to fit residues: 151.6540 Evaluate side-chains 659 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 585 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 281 CYS Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 158 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 43 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 251 optimal weight: 0.0980 chunk 91 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 27 GLN ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN L 160 GLN F 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.166104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.139125 restraints weight = 36250.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.144664 restraints weight = 18046.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.148320 restraints weight = 10423.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.150725 restraints weight = 6679.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.152282 restraints weight = 4671.709| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 21978 Z= 0.273 Angle : 0.759 14.605 29856 Z= 0.402 Chirality : 0.048 0.374 3309 Planarity : 0.005 0.060 3876 Dihedral : 5.688 54.779 3010 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.03 % Favored : 93.86 % Rotamer: Outliers : 3.62 % Allowed : 17.04 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 2754 helix: -0.29 (0.25), residues: 375 sheet: -0.56 (0.17), residues: 876 loop : -1.60 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 150 TYR 0.022 0.002 TYR D 105 PHE 0.028 0.002 PHE H 27 TRP 0.064 0.004 TRP H 36 HIS 0.010 0.002 HIS J 87 Details of bonding type rmsd covalent geometry : bond 0.00590 (21945) covalent geometry : angle 0.75377 (29790) SS BOND : bond 0.00588 ( 33) SS BOND : angle 2.05043 ( 66) hydrogen bonds : bond 0.05124 ( 616) hydrogen bonds : angle 6.66532 ( 1797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 600 time to evaluate : 0.670 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: I 68 PHE cc_start: 0.7624 (m-80) cc_final: 0.6985 (m-80) REVERT: I 83 MET cc_start: 0.5514 (mtp) cc_final: 0.3888 (mtp) REVERT: I 104 SER cc_start: 0.8769 (t) cc_final: 0.8393 (p) REVERT: I 108 TYR cc_start: 0.6245 (m-80) cc_final: 0.5886 (m-80) REVERT: I 117 MET cc_start: 0.7191 (mtm) cc_final: 0.6301 (mtt) REVERT: I 171 TRP cc_start: 0.6709 (m100) cc_final: 0.6365 (m100) REVERT: K 35 TRP cc_start: 0.5636 (m100) cc_final: 0.5332 (m100) REVERT: K 62 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.6865 (m-80) REVERT: K 74 THR cc_start: 0.7954 (m) cc_final: 0.7485 (p) REVERT: K 85 THR cc_start: 0.5269 (m) cc_final: 0.4934 (m) REVERT: K 147 GLN cc_start: 0.6546 (pp30) cc_final: 0.5013 (mp10) REVERT: A 57 ARG cc_start: 0.7601 (ttt90) cc_final: 0.6694 (ttm-80) REVERT: A 82 GLU cc_start: 0.7835 (tp30) cc_final: 0.7320 (tp30) REVERT: A 92 LYS cc_start: 0.8810 (pttp) cc_final: 0.8333 (pttp) REVERT: A 117 THR cc_start: 0.8700 (t) cc_final: 0.8281 (m) REVERT: A 119 GLU cc_start: 0.7485 (tt0) cc_final: 0.6545 (tt0) REVERT: A 121 ILE cc_start: 0.8208 (mp) cc_final: 0.7795 (mm) REVERT: A 123 GLU cc_start: 0.7469 (mm-30) cc_final: 0.6829 (mm-30) REVERT: A 125 PHE cc_start: 0.6657 (m-80) cc_final: 0.6292 (m-10) REVERT: A 150 ARG cc_start: 0.7849 (mmm160) cc_final: 0.7353 (mmm-85) REVERT: A 233 TYR cc_start: 0.6618 (m-80) cc_final: 0.6125 (m-80) REVERT: A 241 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: A 260 MET cc_start: 0.7012 (mmm) cc_final: 0.6352 (mpp) REVERT: A 261 ARG cc_start: 0.7645 (mtt90) cc_final: 0.7221 (mtt90) REVERT: A 268 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7695 (ttm) REVERT: A 275 ASP cc_start: 0.6902 (t70) cc_final: 0.6497 (t70) REVERT: B 51 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7933 (ttmm) REVERT: B 68 LYS cc_start: 0.7199 (mmtp) cc_final: 0.6726 (mmtp) REVERT: B 79 ASP cc_start: 0.7325 (m-30) cc_final: 0.6907 (m-30) REVERT: B 85 GLU cc_start: 0.7171 (tp30) cc_final: 0.6786 (tp30) REVERT: B 94 TYR cc_start: 0.8439 (t80) cc_final: 0.7863 (t80) REVERT: B 121 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7662 (tptp) REVERT: G 3 GLN cc_start: 0.6757 (mp-120) cc_final: 0.6235 (mp10) REVERT: G 68 PHE cc_start: 0.7421 (m-80) cc_final: 0.6894 (m-80) REVERT: G 83 MET cc_start: 0.5091 (OUTLIER) cc_final: 0.3947 (mtp) REVERT: G 160 LYS cc_start: 0.7258 (tppt) cc_final: 0.6857 (tppt) REVERT: J 6 GLN cc_start: 0.6361 (mp10) cc_final: 0.6153 (mp10) REVERT: J 11 VAL cc_start: 0.8573 (p) cc_final: 0.8338 (m) REVERT: J 46 LEU cc_start: 0.5366 (tp) cc_final: 0.4971 (tp) REVERT: J 65 SER cc_start: 0.8144 (t) cc_final: 0.7662 (m) REVERT: J 69 THR cc_start: 0.7248 (p) cc_final: 0.6989 (p) REVERT: J 148 TRP cc_start: 0.5554 (m100) cc_final: 0.5028 (m100) REVERT: C 71 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7885 (mt) REVERT: C 119 GLU cc_start: 0.7537 (tt0) cc_final: 0.7199 (tt0) REVERT: C 132 GLN cc_start: 0.7700 (tt0) cc_final: 0.7043 (tm-30) REVERT: C 153 TRP cc_start: 0.7179 (t60) cc_final: 0.6813 (t60) REVERT: C 189 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7259 (mm-40) REVERT: C 197 GLN cc_start: 0.7240 (pp30) cc_final: 0.6117 (pp30) REVERT: C 208 ARG cc_start: 0.7044 (mtt90) cc_final: 0.6480 (mtt90) REVERT: C 261 ARG cc_start: 0.7777 (mtt90) cc_final: 0.7210 (mtt90) REVERT: E 42 GLN cc_start: 0.7739 (tp40) cc_final: 0.7473 (tp-100) REVERT: E 79 ASP cc_start: 0.7551 (m-30) cc_final: 0.7248 (m-30) REVERT: E 85 GLU cc_start: 0.7422 (tp30) cc_final: 0.7081 (tp30) REVERT: E 91 LEU cc_start: 0.7663 (mt) cc_final: 0.7190 (mt) REVERT: E 95 ASN cc_start: 0.8096 (m-40) cc_final: 0.7690 (m-40) REVERT: E 110 LEU cc_start: 0.7890 (mt) cc_final: 0.7464 (mp) REVERT: H 3 GLN cc_start: 0.6169 (mp10) cc_final: 0.5484 (mp10) REVERT: H 72 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7455 (ttt180) REVERT: H 80 PHE cc_start: 0.6887 (m-80) cc_final: 0.6653 (m-80) REVERT: H 117 MET cc_start: 0.6964 (mtm) cc_final: 0.6140 (mpp) REVERT: H 181 HIS cc_start: 0.6252 (m-70) cc_final: 0.5905 (m-70) REVERT: L 74 THR cc_start: 0.7874 (m) cc_final: 0.7418 (p) REVERT: L 79 GLN cc_start: 0.7369 (mm-40) cc_final: 0.6735 (mm-40) REVERT: L 100 GLN cc_start: 0.7419 (mt0) cc_final: 0.7132 (mt0) REVERT: L 148 TRP cc_start: 0.6377 (m100) cc_final: 0.5960 (m100) REVERT: L 176 SER cc_start: 0.7007 (t) cc_final: 0.6562 (p) REVERT: D 57 ARG cc_start: 0.7960 (ttt90) cc_final: 0.7460 (ttt90) REVERT: D 67 ILE cc_start: 0.7777 (mm) cc_final: 0.7182 (tp) REVERT: D 71 LEU cc_start: 0.7662 (mm) cc_final: 0.7275 (mm) REVERT: D 82 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6398 (mp0) REVERT: D 127 TRP cc_start: 0.8145 (m-10) cc_final: 0.7277 (m-90) REVERT: D 131 THR cc_start: 0.7745 (m) cc_final: 0.7241 (p) REVERT: D 184 HIS cc_start: 0.6829 (m-70) cc_final: 0.6333 (m170) REVERT: D 224 ARG cc_start: 0.7915 (mpt180) cc_final: 0.7487 (mpt-90) REVERT: D 307 LYS cc_start: 0.5684 (mmmt) cc_final: 0.5381 (mmmt) REVERT: F 82 LYS cc_start: 0.8707 (mttp) cc_final: 0.8322 (mptt) REVERT: F 85 GLU cc_start: 0.6876 (tp30) cc_final: 0.6586 (tp30) REVERT: F 89 ILE cc_start: 0.8144 (mt) cc_final: 0.7889 (mt) outliers start: 87 outliers final: 62 residues processed: 638 average time/residue: 0.1542 time to fit residues: 149.2861 Evaluate side-chains 651 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 582 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 188 GLN Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 149 LYS Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 165 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 145 optimal weight: 10.0000 chunk 142 optimal weight: 0.6980 chunk 104 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 253 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 240 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 172 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 27 GLN ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN E 106 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN D 81 ASN F 34 GLN F 106 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.168126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.141178 restraints weight = 36183.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.146772 restraints weight = 17866.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.150456 restraints weight = 10284.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.152881 restraints weight = 6570.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.154427 restraints weight = 4570.167| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.6433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 21978 Z= 0.198 Angle : 0.714 16.026 29856 Z= 0.372 Chirality : 0.046 0.298 3309 Planarity : 0.005 0.057 3876 Dihedral : 5.533 56.324 3010 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.45 % Favored : 94.44 % Rotamer: Outliers : 3.49 % Allowed : 17.87 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.15), residues: 2754 helix: -0.16 (0.25), residues: 366 sheet: -0.55 (0.17), residues: 834 loop : -1.57 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 109 TYR 0.026 0.002 TYR J 173 PHE 0.030 0.002 PHE H 27 TRP 0.054 0.003 TRP H 36 HIS 0.012 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00441 (21945) covalent geometry : angle 0.70977 (29790) SS BOND : bond 0.00464 ( 33) SS BOND : angle 1.78319 ( 66) hydrogen bonds : bond 0.04509 ( 616) hydrogen bonds : angle 6.49780 ( 1797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 583 time to evaluate : 0.783 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: I 68 PHE cc_start: 0.7587 (m-80) cc_final: 0.6940 (m-80) REVERT: I 83 MET cc_start: 0.5529 (mtp) cc_final: 0.3928 (mtp) REVERT: I 104 SER cc_start: 0.8703 (t) cc_final: 0.8403 (p) REVERT: I 108 TYR cc_start: 0.6122 (m-80) cc_final: 0.5790 (m-80) REVERT: I 117 MET cc_start: 0.7090 (mtm) cc_final: 0.6362 (mtt) REVERT: I 171 TRP cc_start: 0.6645 (m100) cc_final: 0.6373 (m100) REVERT: K 4 MET cc_start: 0.5453 (ttp) cc_final: 0.5032 (ppp) REVERT: K 62 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6964 (t80) REVERT: K 74 THR cc_start: 0.7989 (m) cc_final: 0.7206 (p) REVERT: K 147 GLN cc_start: 0.6412 (pp30) cc_final: 0.4931 (mp10) REVERT: K 149 LYS cc_start: 0.7372 (mmmt) cc_final: 0.6976 (mmmt) REVERT: A 57 ARG cc_start: 0.7581 (ttt90) cc_final: 0.6715 (ttm-80) REVERT: A 82 GLU cc_start: 0.7761 (tp30) cc_final: 0.7207 (tp30) REVERT: A 92 LYS cc_start: 0.8831 (pttp) cc_final: 0.8345 (pttp) REVERT: A 119 GLU cc_start: 0.7502 (tt0) cc_final: 0.6682 (tt0) REVERT: A 121 ILE cc_start: 0.8213 (mp) cc_final: 0.7559 (mt) REVERT: A 123 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6915 (mm-30) REVERT: A 125 PHE cc_start: 0.6720 (m-80) cc_final: 0.6354 (m-10) REVERT: A 233 TYR cc_start: 0.6592 (m-80) cc_final: 0.6021 (m-80) REVERT: A 241 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7451 (m-30) REVERT: A 260 MET cc_start: 0.6969 (mmm) cc_final: 0.6735 (mpp) REVERT: A 261 ARG cc_start: 0.7625 (mtt90) cc_final: 0.7299 (mtt90) REVERT: A 268 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7569 (ttm) REVERT: A 275 ASP cc_start: 0.6833 (t70) cc_final: 0.6462 (t70) REVERT: B 17 MET cc_start: 0.3088 (mmm) cc_final: 0.1665 (mmm) REVERT: B 51 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7786 (ttmm) REVERT: B 76 ARG cc_start: 0.7311 (tpt-90) cc_final: 0.6849 (ttt90) REVERT: B 79 ASP cc_start: 0.7276 (m-30) cc_final: 0.6870 (m-30) REVERT: B 85 GLU cc_start: 0.7375 (tp30) cc_final: 0.7079 (tp30) REVERT: B 89 ILE cc_start: 0.8090 (mt) cc_final: 0.7881 (mp) REVERT: B 94 TYR cc_start: 0.8437 (t80) cc_final: 0.7823 (t80) REVERT: B 121 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7682 (tptp) REVERT: G 3 GLN cc_start: 0.6735 (mp-120) cc_final: 0.6216 (mp10) REVERT: G 68 PHE cc_start: 0.7392 (m-80) cc_final: 0.6871 (m-80) REVERT: G 83 MET cc_start: 0.5074 (OUTLIER) cc_final: 0.3892 (mtp) REVERT: G 104 SER cc_start: 0.8211 (t) cc_final: 0.7968 (t) REVERT: J 6 GLN cc_start: 0.6167 (mp10) cc_final: 0.5941 (mt0) REVERT: J 11 VAL cc_start: 0.8590 (p) cc_final: 0.8369 (m) REVERT: J 20 THR cc_start: 0.8453 (m) cc_final: 0.8239 (t) REVERT: J 46 LEU cc_start: 0.5159 (tp) cc_final: 0.4833 (tp) REVERT: J 65 SER cc_start: 0.8054 (t) cc_final: 0.7588 (m) REVERT: J 148 TRP cc_start: 0.5478 (m100) cc_final: 0.4972 (m100) REVERT: C 57 ARG cc_start: 0.7663 (ptm160) cc_final: 0.7364 (ptm160) REVERT: C 71 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7868 (mt) REVERT: C 132 GLN cc_start: 0.7764 (tt0) cc_final: 0.7072 (tm-30) REVERT: C 153 TRP cc_start: 0.7144 (t60) cc_final: 0.6805 (t60) REVERT: C 189 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7236 (mm-40) REVERT: C 197 GLN cc_start: 0.7349 (pp30) cc_final: 0.6270 (pp30) REVERT: C 208 ARG cc_start: 0.7070 (mtt90) cc_final: 0.6459 (mtt90) REVERT: C 261 ARG cc_start: 0.7706 (mtt90) cc_final: 0.7259 (mtt90) REVERT: E 42 GLN cc_start: 0.7796 (tp40) cc_final: 0.7506 (tp-100) REVERT: E 78 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7362 (pt0) REVERT: E 79 ASP cc_start: 0.7448 (m-30) cc_final: 0.7067 (m-30) REVERT: E 85 GLU cc_start: 0.7368 (tp30) cc_final: 0.7083 (tp30) REVERT: E 91 LEU cc_start: 0.7552 (mt) cc_final: 0.7140 (mt) REVERT: E 95 ASN cc_start: 0.8045 (m-40) cc_final: 0.7473 (m-40) REVERT: H 3 GLN cc_start: 0.6106 (mp10) cc_final: 0.5456 (mp10) REVERT: H 72 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7511 (ttt180) REVERT: H 80 PHE cc_start: 0.6716 (m-80) cc_final: 0.6374 (m-80) REVERT: H 117 MET cc_start: 0.7027 (mtm) cc_final: 0.6260 (mpp) REVERT: H 181 HIS cc_start: 0.5903 (m-70) cc_final: 0.5694 (m-70) REVERT: L 20 THR cc_start: 0.8668 (m) cc_final: 0.8273 (t) REVERT: L 27 GLN cc_start: 0.6283 (pp30) cc_final: 0.6056 (pp30) REVERT: L 74 THR cc_start: 0.7733 (m) cc_final: 0.7267 (p) REVERT: L 148 TRP cc_start: 0.6340 (m100) cc_final: 0.5907 (m100) REVERT: L 176 SER cc_start: 0.6956 (t) cc_final: 0.6516 (p) REVERT: D 57 ARG cc_start: 0.7945 (ttt90) cc_final: 0.7450 (ttm-80) REVERT: D 67 ILE cc_start: 0.7764 (mm) cc_final: 0.7347 (tp) REVERT: D 82 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6036 (mp0) REVERT: D 127 TRP cc_start: 0.7990 (m-10) cc_final: 0.7464 (m-90) REVERT: D 131 THR cc_start: 0.7703 (m) cc_final: 0.7197 (p) REVERT: D 150 ARG cc_start: 0.8006 (mmm160) cc_final: 0.7513 (mmm160) REVERT: D 184 HIS cc_start: 0.6774 (m-70) cc_final: 0.6285 (m170) REVERT: D 224 ARG cc_start: 0.7900 (mpt180) cc_final: 0.7436 (mpt-90) REVERT: D 307 LYS cc_start: 0.5581 (mmmt) cc_final: 0.5067 (mmmt) REVERT: F 82 LYS cc_start: 0.8697 (mttp) cc_final: 0.8279 (mptt) REVERT: F 85 GLU cc_start: 0.6919 (tp30) cc_final: 0.6419 (tp30) REVERT: F 89 ILE cc_start: 0.8127 (mt) cc_final: 0.7847 (mt) outliers start: 84 outliers final: 65 residues processed: 622 average time/residue: 0.1665 time to fit residues: 157.2068 Evaluate side-chains 647 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 574 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 149 LYS Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 165 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 29 optimal weight: 9.9990 chunk 226 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 228 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 253 optimal weight: 0.3980 chunk 242 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 27 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN J 90 GLN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN D 81 ASN F 42 GLN F 106 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.170130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.143450 restraints weight = 36313.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.149050 restraints weight = 17965.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.152705 restraints weight = 10334.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.155131 restraints weight = 6598.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.156709 restraints weight = 4574.374| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 21978 Z= 0.148 Angle : 0.696 16.605 29856 Z= 0.358 Chirality : 0.046 0.331 3309 Planarity : 0.005 0.058 3876 Dihedral : 5.321 56.717 3010 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.72 % Favored : 95.17 % Rotamer: Outliers : 3.24 % Allowed : 18.41 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.15), residues: 2754 helix: -0.16 (0.25), residues: 366 sheet: -0.41 (0.18), residues: 813 loop : -1.46 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 103 TYR 0.025 0.001 TYR J 173 PHE 0.029 0.002 PHE H 27 TRP 0.043 0.002 TRP H 36 HIS 0.006 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00342 (21945) covalent geometry : angle 0.69256 (29790) SS BOND : bond 0.00355 ( 33) SS BOND : angle 1.56274 ( 66) hydrogen bonds : bond 0.04146 ( 616) hydrogen bonds : angle 6.36311 ( 1797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 580 time to evaluate : 0.963 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: I 68 PHE cc_start: 0.7469 (m-80) cc_final: 0.7076 (m-80) REVERT: I 70 ILE cc_start: 0.8345 (pt) cc_final: 0.8013 (mp) REVERT: I 83 MET cc_start: 0.5333 (mtp) cc_final: 0.3788 (mtp) REVERT: I 104 SER cc_start: 0.8735 (t) cc_final: 0.8490 (p) REVERT: I 108 TYR cc_start: 0.6090 (m-80) cc_final: 0.5756 (m-80) REVERT: I 117 MET cc_start: 0.7095 (mtm) cc_final: 0.6681 (mtt) REVERT: I 171 TRP cc_start: 0.6490 (m100) cc_final: 0.6235 (m100) REVERT: K 4 MET cc_start: 0.5466 (ttp) cc_final: 0.5160 (ppp) REVERT: K 62 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.7014 (t80) REVERT: K 85 THR cc_start: 0.4969 (m) cc_final: 0.4550 (m) REVERT: K 147 GLN cc_start: 0.6296 (pp30) cc_final: 0.4953 (mp10) REVERT: A 57 ARG cc_start: 0.7570 (ttt90) cc_final: 0.6762 (ttm-80) REVERT: A 82 GLU cc_start: 0.7647 (tp30) cc_final: 0.7137 (tp30) REVERT: A 92 LYS cc_start: 0.8768 (pttp) cc_final: 0.8331 (pttp) REVERT: A 119 GLU cc_start: 0.7536 (tt0) cc_final: 0.6648 (tt0) REVERT: A 121 ILE cc_start: 0.8293 (mp) cc_final: 0.7981 (mm) REVERT: A 123 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6600 (mm-30) REVERT: A 125 PHE cc_start: 0.6597 (m-80) cc_final: 0.6255 (m-10) REVERT: A 223 VAL cc_start: 0.7391 (t) cc_final: 0.7150 (p) REVERT: A 233 TYR cc_start: 0.6494 (m-80) cc_final: 0.5972 (m-80) REVERT: A 241 ASP cc_start: 0.7808 (m-30) cc_final: 0.7434 (m-30) REVERT: A 261 ARG cc_start: 0.7563 (mtt90) cc_final: 0.7253 (mtt90) REVERT: A 268 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7511 (ttm) REVERT: A 271 ASP cc_start: 0.6151 (m-30) cc_final: 0.5865 (m-30) REVERT: A 275 ASP cc_start: 0.6865 (t70) cc_final: 0.6519 (t70) REVERT: B 17 MET cc_start: 0.3028 (mmm) cc_final: 0.2114 (mmm) REVERT: B 51 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7630 (ttmm) REVERT: B 76 ARG cc_start: 0.7275 (tpt-90) cc_final: 0.6819 (ttt90) REVERT: B 79 ASP cc_start: 0.7017 (m-30) cc_final: 0.6644 (m-30) REVERT: B 85 GLU cc_start: 0.7076 (tp30) cc_final: 0.6821 (tp30) REVERT: B 94 TYR cc_start: 0.8378 (t80) cc_final: 0.7783 (t80) REVERT: B 121 LYS cc_start: 0.8052 (ttpt) cc_final: 0.7592 (tptp) REVERT: G 3 GLN cc_start: 0.6733 (mp-120) cc_final: 0.6232 (mp10) REVERT: G 68 PHE cc_start: 0.7268 (m-80) cc_final: 0.6784 (m-80) REVERT: G 83 MET cc_start: 0.4859 (OUTLIER) cc_final: 0.3622 (mtp) REVERT: G 94 TYR cc_start: 0.4567 (m-80) cc_final: 0.4057 (m-10) REVERT: G 104 SER cc_start: 0.8242 (t) cc_final: 0.8015 (t) REVERT: G 160 LYS cc_start: 0.7129 (tppt) cc_final: 0.6862 (tppt) REVERT: J 11 VAL cc_start: 0.8600 (p) cc_final: 0.8380 (m) REVERT: J 20 THR cc_start: 0.8397 (m) cc_final: 0.8178 (t) REVERT: J 46 LEU cc_start: 0.5532 (tp) cc_final: 0.5275 (tp) REVERT: J 65 SER cc_start: 0.8009 (t) cc_final: 0.7799 (t) REVERT: J 179 LEU cc_start: 0.7878 (mt) cc_final: 0.7351 (mm) REVERT: C 57 ARG cc_start: 0.7820 (ptm160) cc_final: 0.7533 (ptm160) REVERT: C 71 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7789 (mt) REVERT: C 132 GLN cc_start: 0.7793 (tt0) cc_final: 0.7091 (tm-30) REVERT: C 153 TRP cc_start: 0.7042 (t60) cc_final: 0.6698 (t60) REVERT: C 189 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7219 (mm-40) REVERT: C 197 GLN cc_start: 0.6963 (pp30) cc_final: 0.5887 (pp30) REVERT: C 259 LYS cc_start: 0.7792 (mttt) cc_final: 0.7451 (mttt) REVERT: C 261 ARG cc_start: 0.7584 (mtt90) cc_final: 0.7193 (mtt90) REVERT: C 268 MET cc_start: 0.7370 (ttm) cc_final: 0.7168 (ttp) REVERT: E 42 GLN cc_start: 0.7712 (tp40) cc_final: 0.7416 (tp-100) REVERT: E 79 ASP cc_start: 0.7217 (m-30) cc_final: 0.6896 (m-30) REVERT: E 82 LYS cc_start: 0.8394 (mttm) cc_final: 0.8115 (mttt) REVERT: E 85 GLU cc_start: 0.7208 (tp30) cc_final: 0.6923 (tp30) REVERT: E 91 LEU cc_start: 0.7495 (mt) cc_final: 0.7061 (mt) REVERT: E 95 ASN cc_start: 0.8037 (m-40) cc_final: 0.7490 (m-40) REVERT: H 3 GLN cc_start: 0.6164 (mp10) cc_final: 0.5458 (mp10) REVERT: H 65 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8354 (tppp) REVERT: H 72 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7592 (ttt180) REVERT: H 80 PHE cc_start: 0.6637 (m-80) cc_final: 0.6242 (m-80) REVERT: H 117 MET cc_start: 0.6862 (mtm) cc_final: 0.6265 (mpp) REVERT: L 20 THR cc_start: 0.8665 (m) cc_final: 0.8358 (p) REVERT: L 27 GLN cc_start: 0.6027 (pp30) cc_final: 0.5747 (pp30) REVERT: L 74 THR cc_start: 0.7670 (m) cc_final: 0.7342 (p) REVERT: L 148 TRP cc_start: 0.6313 (m100) cc_final: 0.5948 (m100) REVERT: L 176 SER cc_start: 0.6925 (t) cc_final: 0.6500 (p) REVERT: D 57 ARG cc_start: 0.7943 (ttt90) cc_final: 0.7464 (ttt90) REVERT: D 67 ILE cc_start: 0.7849 (mm) cc_final: 0.7511 (tp) REVERT: D 81 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.7145 (t0) REVERT: D 82 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6356 (mp0) REVERT: D 131 THR cc_start: 0.7644 (m) cc_final: 0.7194 (p) REVERT: D 150 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7651 (mmm160) REVERT: D 184 HIS cc_start: 0.6734 (m-70) cc_final: 0.6244 (m170) REVERT: D 224 ARG cc_start: 0.7885 (mpt180) cc_final: 0.7577 (mpt-90) REVERT: D 307 LYS cc_start: 0.5436 (mmmt) cc_final: 0.5002 (mmmt) REVERT: F 42 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7344 (tp40) REVERT: F 89 ILE cc_start: 0.7977 (mt) cc_final: 0.7494 (mt) REVERT: F 121 LYS cc_start: 0.8011 (tptp) cc_final: 0.7801 (tptp) outliers start: 78 outliers final: 62 residues processed: 617 average time/residue: 0.1676 time to fit residues: 156.6415 Evaluate side-chains 641 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 570 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 90 GLN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 149 LYS Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 165 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 264 optimal weight: 1.9990 chunk 157 optimal weight: 0.0970 chunk 91 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 200 optimal weight: 0.2980 chunk 179 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 27 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN F 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.170571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.143817 restraints weight = 35988.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.149449 restraints weight = 17860.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.153146 restraints weight = 10304.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.155555 restraints weight = 6584.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.157127 restraints weight = 4573.195| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 21978 Z= 0.153 Angle : 0.707 15.630 29856 Z= 0.364 Chirality : 0.046 0.338 3309 Planarity : 0.005 0.063 3876 Dihedral : 5.281 57.088 3010 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.72 % Favored : 95.17 % Rotamer: Outliers : 2.99 % Allowed : 18.70 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 2754 helix: -0.26 (0.25), residues: 372 sheet: -0.24 (0.18), residues: 828 loop : -1.41 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 103 TYR 0.021 0.001 TYR J 173 PHE 0.028 0.002 PHE H 27 TRP 0.036 0.002 TRP B 14 HIS 0.011 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00356 (21945) covalent geometry : angle 0.70403 (29790) SS BOND : bond 0.00345 ( 33) SS BOND : angle 1.51528 ( 66) hydrogen bonds : bond 0.04132 ( 616) hydrogen bonds : angle 6.31093 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5173.61 seconds wall clock time: 89 minutes 46.16 seconds (5386.16 seconds total)