Starting phenix.real_space_refine on Fri Mar 6 02:30:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ekq_31173/03_2026/7ekq_31173.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ekq_31173/03_2026/7ekq_31173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ekq_31173/03_2026/7ekq_31173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ekq_31173/03_2026/7ekq_31173.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ekq_31173/03_2026/7ekq_31173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ekq_31173/03_2026/7ekq_31173.map" } resolution = 3.6 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= 0.021 sd= 0.138 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 164 5.16 5 C 17502 2.51 5 N 4719 2.21 5 O 5278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.03s 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: 27663 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1763 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "B" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1477 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 7, 'TRANS': 185} Chain: "C" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1329 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "D" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1477 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 7, 'TRANS': 185} Chain: "E" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1329 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "F" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1307 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 5, 'TRANS': 166} Chain: "G" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1369 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain: "H" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1131 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "I" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1745 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 14, 'TRANS': 202} Chain: "J" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1279 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain: "K" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1841 Classifications: {'peptide': 233} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 217} Chain: "L" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1494 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Chain: "M" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1014 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "N" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2691 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 23, 'TRANS': 314} Chain: "O" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1259 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "P" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 713 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "Q" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1567 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 188} Chain breaks: 1 Chain: "R" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1439 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 184} Chain: "S" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1439 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 184} Time building chain proxies: 6.50, per 1000 atoms: 0.23 Number of scatterers: 27663 At special positions: 0 Unit cell: (166.068, 163.432, 127.846, 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 164 16.00 O 5278 8.00 N 4719 7.00 C 17502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 885.7 milliseconds 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6574 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 47 sheets defined 40.9% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 31 through 39 Processing helix chain 'A' and resid 49 through 67 removed outlier: 3.975A pdb=" N THR A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 removed outlier: 3.834A pdb=" N VAL A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 118 removed outlier: 3.802A pdb=" N VAL A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 170 removed outlier: 3.685A pdb=" N ALA A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 removed outlier: 3.541A pdb=" N ILE A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.968A pdb=" N LEU A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 Processing helix chain 'B' and resid 43 through 58 removed outlier: 3.852A pdb=" N ILE B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 58 " --> pdb=" O VAL B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 88 removed outlier: 3.507A pdb=" N ASN B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 87 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.713A pdb=" N GLY B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG B 115 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 139 Processing helix chain 'B' and resid 165 through 192 removed outlier: 3.861A pdb=" N GLU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 183 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.606A pdb=" N THR B 199 " --> pdb=" O MET B 195 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 removed outlier: 3.854A pdb=" N ILE B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.838A pdb=" N ARG C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 52 removed outlier: 3.575A pdb=" N ASP C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 46 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 80 removed outlier: 4.268A pdb=" N GLY C 73 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 103 removed outlier: 3.579A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 152 removed outlier: 3.680A pdb=" N ILE C 133 " --> pdb=" O GLN C 129 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 135 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 140 " --> pdb=" O GLN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 164 removed outlier: 3.744A pdb=" N GLU C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 removed outlier: 4.142A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 59 removed outlier: 4.340A pdb=" N GLU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 82 removed outlier: 3.598A pdb=" N ASN D 75 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 76 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 115 removed outlier: 3.521A pdb=" N ALA D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG D 115 " --> pdb=" O PHE D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 139 Processing helix chain 'D' and resid 165 through 192 removed outlier: 3.773A pdb=" N GLU D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 176 " --> pdb=" O GLN D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 202 removed outlier: 3.771A pdb=" N ILE D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D 199 " --> pdb=" O MET D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 217 removed outlier: 4.689A pdb=" N GLU D 215 " --> pdb=" O GLN D 211 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 24 Processing helix chain 'E' and resid 36 through 52 removed outlier: 3.603A pdb=" N ILE E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 48 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER E 50 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 removed outlier: 3.916A pdb=" N ILE E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR E 75 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP E 76 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 102 removed outlier: 3.743A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 152 removed outlier: 3.514A pdb=" N GLU E 134 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E 149 " --> pdb=" O ALA E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 166 removed outlier: 3.567A pdb=" N GLU E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR E 166 " --> pdb=" O ILE E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 180 removed outlier: 3.577A pdb=" N LYS E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU E 179 " --> pdb=" O LEU E 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 60 removed outlier: 4.159A pdb=" N GLN F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 55 through 60' Processing helix chain 'F' and resid 70 through 88 removed outlier: 3.720A pdb=" N TYR F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP F 85 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER F 86 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 116 removed outlier: 3.673A pdb=" N GLY F 107 " --> pdb=" O SER F 103 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP F 112 " --> pdb=" O MET F 108 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET F 114 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG F 115 " --> pdb=" O PHE F 111 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 139 removed outlier: 3.749A pdb=" N ILE F 136 " --> pdb=" O MET F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 192 removed outlier: 3.749A pdb=" N GLU F 170 " --> pdb=" O ALA F 166 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 171 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU F 175 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN F 189 " --> pdb=" O GLY F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 202 removed outlier: 3.898A pdb=" N ILE F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR F 199 " --> pdb=" O MET F 195 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 202 " --> pdb=" O ILE F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 217 removed outlier: 4.391A pdb=" N GLU F 215 " --> pdb=" O GLN F 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 24 removed outlier: 3.504A pdb=" N ARG G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN G 24 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 52 removed outlier: 3.947A pdb=" N ASP G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA G 40 " --> pdb=" O PHE G 36 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU G 47 " --> pdb=" O SER G 43 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU G 48 " --> pdb=" O GLN G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 81 removed outlier: 3.666A pdb=" N MET G 72 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY G 73 " --> pdb=" O THR G 69 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 103 removed outlier: 3.673A pdb=" N GLY G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA G 103 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 152 removed outlier: 3.743A pdb=" N GLU G 134 " --> pdb=" O ALA G 130 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE G 135 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN G 136 " --> pdb=" O ASP G 132 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 166 removed outlier: 4.003A pdb=" N GLU G 164 " --> pdb=" O SER G 160 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR G 166 " --> pdb=" O ILE G 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 370 removed outlier: 3.709A pdb=" N GLY H 362 " --> pdb=" O SER H 358 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR H 364 " --> pdb=" O GLY H 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL H 365 " --> pdb=" O ASN H 361 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN H 370 " --> pdb=" O HIS H 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 394 Processing helix chain 'H' and resid 420 through 446 removed outlier: 3.862A pdb=" N ILE H 424 " --> pdb=" O GLN H 420 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP H 425 " --> pdb=" O ALA H 421 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE H 426 " --> pdb=" O SER H 422 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP H 427 " --> pdb=" O ASP H 423 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN H 429 " --> pdb=" O TRP H 425 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE H 441 " --> pdb=" O ASP H 437 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 457 removed outlier: 3.651A pdb=" N LEU H 454 " --> pdb=" O ARG H 450 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG H 455 " --> pdb=" O HIS H 451 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP H 456 " --> pdb=" O LYS H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 472 removed outlier: 3.572A pdb=" N THR H 468 " --> pdb=" O THR H 464 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE H 469 " --> pdb=" O ALA H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 490 removed outlier: 3.640A pdb=" N SER H 485 " --> pdb=" O GLU H 481 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE H 486 " --> pdb=" O VAL H 482 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU H 488 " --> pdb=" O HIS H 484 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR H 490 " --> pdb=" O ILE H 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 35 Processing helix chain 'I' and resid 48 through 60 removed outlier: 3.906A pdb=" N VAL I 52 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL I 53 " --> pdb=" O THR I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 101 removed outlier: 3.859A pdb=" N ALA I 95 " --> pdb=" O ASN I 91 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 124 removed outlier: 3.646A pdb=" N LEU I 122 " --> pdb=" O GLN I 118 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 179 removed outlier: 3.508A pdb=" N GLN I 157 " --> pdb=" O ALA I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 189 removed outlier: 3.670A pdb=" N CYS I 185 " --> pdb=" O ASP I 181 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN I 186 " --> pdb=" O LEU I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 205 removed outlier: 3.721A pdb=" N TYR I 202 " --> pdb=" O VAL I 198 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU I 203 " --> pdb=" O LYS I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'J' and resid 358 through 368 removed outlier: 3.852A pdb=" N GLY J 362 " --> pdb=" O SER J 358 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE J 363 " --> pdb=" O VAL J 359 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 394 removed outlier: 4.055A pdb=" N LEU J 390 " --> pdb=" O SER J 386 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA J 391 " --> pdb=" O ALA J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 446 removed outlier: 4.091A pdb=" N ILE J 426 " --> pdb=" O SER J 422 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP J 427 " --> pdb=" O ASP J 423 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER J 428 " --> pdb=" O ILE J 424 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU J 430 " --> pdb=" O ILE J 426 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR J 446 " --> pdb=" O TYR J 442 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 455 removed outlier: 3.643A pdb=" N ILE J 453 " --> pdb=" O PRO J 449 " (cutoff:3.500A) Processing helix chain 'J' and resid 464 through 472 removed outlier: 3.692A pdb=" N ILE J 469 " --> pdb=" O ALA J 465 " (cutoff:3.500A) Processing helix chain 'J' and resid 479 through 509 removed outlier: 3.696A pdb=" N HIS J 484 " --> pdb=" O ASN J 480 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER J 485 " --> pdb=" O GLU J 481 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN J 492 " --> pdb=" O GLU J 488 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL J 493 " --> pdb=" O MET J 489 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP J 494 " --> pdb=" O THR J 490 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS J 497 " --> pdb=" O VAL J 493 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS J 500 " --> pdb=" O TYR J 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 13 removed outlier: 3.503A pdb=" N LEU K 10 " --> pdb=" O LEU K 6 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP K 11 " --> pdb=" O ARG K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 27 removed outlier: 3.733A pdb=" N ARG K 23 " --> pdb=" O ASP K 19 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU K 27 " --> pdb=" O ARG K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 55 removed outlier: 3.950A pdb=" N GLU K 42 " --> pdb=" O SER K 38 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN K 53 " --> pdb=" O PHE K 49 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU K 54 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 90 removed outlier: 3.526A pdb=" N MET K 88 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY K 90 " --> pdb=" O SER K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 111 Processing helix chain 'K' and resid 145 through 169 removed outlier: 3.601A pdb=" N LYS K 151 " --> pdb=" O ASP K 147 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR K 157 " --> pdb=" O THR K 153 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS K 167 " --> pdb=" O TYR K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 178 removed outlier: 3.766A pdb=" N ILE K 175 " --> pdb=" O THR K 171 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET K 176 " --> pdb=" O GLU K 172 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP K 178 " --> pdb=" O GLN K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 194 Processing helix chain 'K' and resid 210 through 214 removed outlier: 3.919A pdb=" N LYS K 214 " --> pdb=" O ASP K 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 61 Processing helix chain 'L' and resid 71 through 89 removed outlier: 3.557A pdb=" N ASN L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN L 77 " --> pdb=" O ASP L 73 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA L 80 " --> pdb=" O ASN L 76 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU L 83 " --> pdb=" O ILE L 79 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP L 89 " --> pdb=" O LEU L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 117 removed outlier: 3.522A pdb=" N LEU L 110 " --> pdb=" O PRO L 106 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR L 113 " --> pdb=" O ALA L 109 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET L 114 " --> pdb=" O LEU L 110 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN L 115 " --> pdb=" O TYR L 111 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL L 117 " --> pdb=" O THR L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 134 removed outlier: 3.511A pdb=" N GLY L 134 " --> pdb=" O GLY L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 139 Processing helix chain 'L' and resid 166 through 193 removed outlier: 3.671A pdb=" N HIS L 171 " --> pdb=" O ALA L 167 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE L 172 " --> pdb=" O SER L 168 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR L 183 " --> pdb=" O ARG L 179 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR L 188 " --> pdb=" O LEU L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 203 removed outlier: 3.611A pdb=" N VAL L 199 " --> pdb=" O PRO L 195 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE L 200 " --> pdb=" O TYR L 196 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG L 201 " --> pdb=" O ASP L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 217 removed outlier: 4.230A pdb=" N GLU L 216 " --> pdb=" O LYS L 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 371 removed outlier: 3.693A pdb=" N THR M 364 " --> pdb=" O GLY M 360 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU M 369 " --> pdb=" O VAL M 365 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN M 370 " --> pdb=" O HIS M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 394 removed outlier: 3.591A pdb=" N LEU M 390 " --> pdb=" O SER M 386 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA M 391 " --> pdb=" O ALA M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 420 through 447 removed outlier: 3.923A pdb=" N ILE M 424 " --> pdb=" O GLN M 420 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TRP M 425 " --> pdb=" O ALA M 421 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN M 429 " --> pdb=" O TRP M 425 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU M 444 " --> pdb=" O GLU M 440 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER M 445 " --> pdb=" O ILE M 441 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR M 447 " --> pdb=" O SER M 443 " (cutoff:3.500A) Processing helix chain 'M' and resid 449 through 457 removed outlier: 3.874A pdb=" N ILE M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG M 455 " --> pdb=" O HIS M 451 " (cutoff:3.500A) Processing helix chain 'M' and resid 466 through 471 removed outlier: 3.868A pdb=" N TYR M 470 " --> pdb=" O MET M 466 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 27 removed outlier: 3.582A pdb=" N GLN N 27 " --> pdb=" O LEU N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 54 removed outlier: 3.852A pdb=" N GLU N 42 " --> pdb=" O PRO N 38 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU N 43 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN N 54 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 93 removed outlier: 3.568A pdb=" N ALA N 85 " --> pdb=" O SER N 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR N 87 " --> pdb=" O GLY N 83 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR N 89 " --> pdb=" O ALA N 85 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET N 90 " --> pdb=" O LEU N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 115 Processing helix chain 'N' and resid 144 through 170 removed outlier: 4.076A pdb=" N HIS N 148 " --> pdb=" O ALA N 144 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE N 149 " --> pdb=" O ILE N 145 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY N 168 " --> pdb=" O MET N 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 180 removed outlier: 3.789A pdb=" N ALA N 178 " --> pdb=" O ASP N 174 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP N 179 " --> pdb=" O LYS N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 195 Processing helix chain 'N' and resid 204 through 218 removed outlier: 3.661A pdb=" N TRP N 215 " --> pdb=" O ALA N 211 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE N 216 " --> pdb=" O ALA N 212 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 224 removed outlier: 4.232A pdb=" N GLU N 224 " --> pdb=" O ARG N 220 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 263 removed outlier: 3.631A pdb=" N GLN N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU N 232 " --> pdb=" O GLU N 228 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP N 244 " --> pdb=" O TYR N 240 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER N 245 " --> pdb=" O ALA N 241 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET N 250 " --> pdb=" O PHE N 246 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR N 251 " --> pdb=" O ARG N 247 " (cutoff:3.500A) Processing helix chain 'N' and resid 269 through 277 removed outlier: 4.011A pdb=" N MET N 273 " --> pdb=" O SER N 269 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU N 274 " --> pdb=" O SER N 270 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN N 275 " --> pdb=" O ARG N 271 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL N 276 " --> pdb=" O ASN N 272 " (cutoff:3.500A) Processing helix chain 'O' and resid 1 through 6 removed outlier: 4.269A pdb=" N THR O 4 " --> pdb=" O ALA O 1 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA O 6 " --> pdb=" O ALA O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 12 Processing helix chain 'O' and resid 16 through 33 removed outlier: 3.593A pdb=" N SER O 21 " --> pdb=" O ALA O 17 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE O 23 " --> pdb=" O ALA O 19 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE O 29 " --> pdb=" O TYR O 25 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA O 30 " --> pdb=" O ALA O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 50 removed outlier: 3.731A pdb=" N GLY O 46 " --> pdb=" O MET O 42 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE O 47 " --> pdb=" O VAL O 43 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU O 48 " --> pdb=" O LEU O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 3.739A pdb=" N LEU O 59 " --> pdb=" O ALA O 55 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER O 61 " --> pdb=" O LYS O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 81 removed outlier: 3.790A pdb=" N ALA O 70 " --> pdb=" O ASP O 66 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL O 74 " --> pdb=" O ALA O 70 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU O 75 " --> pdb=" O TRP O 71 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN O 79 " --> pdb=" O LEU O 75 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL O 80 " --> pdb=" O TRP O 76 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS O 81 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 114 removed outlier: 3.812A pdb=" N LYS O 101 " --> pdb=" O ASP O 97 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL O 102 " --> pdb=" O ARG O 98 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE O 103 " --> pdb=" O ALA O 99 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL O 111 " --> pdb=" O SER O 107 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP O 112 " --> pdb=" O ASP O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 131 removed outlier: 3.890A pdb=" N VAL O 123 " --> pdb=" O TYR O 119 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU O 124 " --> pdb=" O SER O 120 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY O 130 " --> pdb=" O ALA O 126 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY O 131 " --> pdb=" O LEU O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 137 removed outlier: 3.811A pdb=" N ASP O 135 " --> pdb=" O GLY O 131 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU O 136 " --> pdb=" O VAL O 132 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 156 removed outlier: 3.547A pdb=" N VAL O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS O 149 " --> pdb=" O GLU O 145 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL O 151 " --> pdb=" O VAL O 147 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU O 152 " --> pdb=" O ARG O 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS O 153 " --> pdb=" O LYS O 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 38 removed outlier: 3.550A pdb=" N GLY P 36 " --> pdb=" O LYS P 33 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY P 37 " --> pdb=" O THR P 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 removed outlier: 4.426A pdb=" N LYS R 28 " --> pdb=" O GLU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 101 removed outlier: 3.642A pdb=" N GLN R 100 " --> pdb=" O LYS R 97 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 101 removed outlier: 3.518A pdb=" N GLN S 100 " --> pdb=" O LYS S 97 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU S 101 " --> pdb=" O ILE S 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 97 through 101' Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 45 removed outlier: 6.245A pdb=" N ILE A 42 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ASN A 77 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE A 44 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE A 72 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL A 103 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU A 105 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE A 76 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ALA A 107 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 78 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N TYR A 125 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR A 102 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.262A pdb=" N HIS A 185 " --> pdb=" O MET A 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 66 removed outlier: 6.611A pdb=" N VAL B 63 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASN B 98 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU B 65 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N TYR B 146 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR B 123 " --> pdb=" O TYR B 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA7, first strand: chain 'C' and resid 26 through 30 removed outlier: 6.104A pdb=" N ILE C 57 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR C 88 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE C 59 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE C 90 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE C 61 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU C 92 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 94 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG C 116 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLY C 91 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N MET C 118 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA C 93 " --> pdb=" O MET C 118 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG C 170 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 26 through 30 removed outlier: 6.104A pdb=" N ILE C 57 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR C 88 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE C 59 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE C 90 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE C 61 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU C 92 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 94 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASN C 110 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR C 87 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER C 111 " --> pdb=" O HIS C 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 62 through 64 removed outlier: 6.335A pdb=" N VAL D 63 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ASN D 98 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU D 128 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE D 206 " --> pdb=" O ILE D 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 62 through 64 removed outlier: 6.335A pdb=" N VAL D 63 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ASN D 98 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU D 128 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N TYR D 146 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR D 123 " --> pdb=" O TYR D 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 160 through 164 removed outlier: 3.666A pdb=" N GLY D 160 " --> pdb=" O GLY M 419 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY D 164 " --> pdb=" O GLY M 415 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY M 415 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 26 through 30 removed outlier: 6.289A pdb=" N VAL E 27 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASN E 62 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU E 29 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE E 57 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N TYR E 88 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE E 59 " --> pdb=" O TYR E 88 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE E 61 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU E 92 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG E 116 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLY E 91 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N MET E 118 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ALA E 93 " --> pdb=" O MET E 118 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG E 170 " --> pdb=" O ILE E 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 26 through 30 removed outlier: 6.289A pdb=" N VAL E 27 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASN E 62 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU E 29 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE E 57 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N TYR E 88 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE E 59 " --> pdb=" O TYR E 88 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE E 61 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU E 92 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ASN E 110 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR E 87 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 62 through 66 removed outlier: 7.184A pdb=" N VAL F 63 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ASN F 98 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU F 65 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N MET F 95 " --> pdb=" O CYS F 124 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE F 126 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL F 97 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU F 128 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N THR F 123 " --> pdb=" O TYR F 146 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 62 through 66 removed outlier: 7.184A pdb=" N VAL F 63 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ASN F 98 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU F 65 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N MET F 95 " --> pdb=" O CYS F 124 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE F 126 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL F 97 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU F 128 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARG F 152 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY F 127 " --> pdb=" O ARG F 152 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N MET F 154 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA F 129 " --> pdb=" O MET F 154 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE F 206 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 26 through 30 removed outlier: 6.114A pdb=" N ILE G 57 " --> pdb=" O ASN G 86 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N TYR G 88 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE G 59 " --> pdb=" O TYR G 88 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE G 61 " --> pdb=" O PHE G 90 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU G 92 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ASN G 110 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N THR G 87 " --> pdb=" O ASN G 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 117 through 118 Processing sheet with id=AB9, first strand: chain 'G' and resid 124 through 126 removed outlier: 4.451A pdb=" N GLY G 124 " --> pdb=" O GLY J 419 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY J 419 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA G 126 " --> pdb=" O LEU J 417 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU J 417 " --> pdb=" O ALA G 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'H' and resid 347 through 352 removed outlier: 3.653A pdb=" N MET H 350 " --> pdb=" O LEU H 377 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU H 379 " --> pdb=" O MET H 350 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL H 402 " --> pdb=" O GLU H 476 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 408 through 410 Processing sheet with id=AC3, first strand: chain 'I' and resid 37 through 40 removed outlier: 5.861A pdb=" N ILE I 70 " --> pdb=" O TYR I 108 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLY I 110 " --> pdb=" O ILE I 70 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL I 72 " --> pdb=" O GLY I 110 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR I 112 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N LEU I 74 " --> pdb=" O THR I 112 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS I 114 " --> pdb=" O LEU I 74 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER I 76 " --> pdb=" O LYS I 114 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N TYR I 132 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR I 109 " --> pdb=" O TYR I 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 139 through 141 removed outlier: 3.776A pdb=" N THR I 141 " --> pdb=" O ARG I 194 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG I 194 " --> pdb=" O THR I 141 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 348 through 352 removed outlier: 3.722A pdb=" N THR J 403 " --> pdb=" O ALA J 380 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG J 400 " --> pdb=" O GLU J 476 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA J 478 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL J 402 " --> pdb=" O ALA J 478 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 383 through 384 removed outlier: 6.115A pdb=" N ALA J 384 " --> pdb=" O MET J 409 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE J 410 " --> pdb=" O PHE J 461 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE J 461 " --> pdb=" O ILE J 410 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'K' and resid 29 through 32 removed outlier: 5.317A pdb=" N SER K 65 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASN K 104 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N MET K 130 " --> pdb=" O GLY K 103 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA K 105 " --> pdb=" O MET K 130 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE K 129 " --> pdb=" O PHE K 185 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 29 through 32 removed outlier: 5.317A pdb=" N SER K 65 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASN K 104 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ALA K 122 " --> pdb=" O ILE K 97 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR K 99 " --> pdb=" O ALA K 122 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG K 121 " --> pdb=" O THR K 198 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AD1, first strand: chain 'L' and resid 63 through 66 removed outlier: 5.879A pdb=" N ILE L 93 " --> pdb=" O ALA L 122 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL L 124 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TYR L 95 " --> pdb=" O VAL L 124 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 128 through 129 removed outlier: 3.520A pdb=" N MET L 155 " --> pdb=" O CYS L 129 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS L 207 " --> pdb=" O MET L 156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 348 through 354 removed outlier: 6.586A pdb=" N VAL M 348 " --> pdb=" O LEU M 377 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU M 379 " --> pdb=" O VAL M 348 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET M 350 " --> pdb=" O LEU M 379 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU M 381 " --> pdb=" O MET M 350 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE M 352 " --> pdb=" O LEU M 381 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL M 383 " --> pdb=" O ILE M 352 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N HIS M 407 " --> pdb=" O ALA M 380 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLY M 382 " --> pdb=" O HIS M 407 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N MET M 409 " --> pdb=" O GLY M 382 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA M 384 " --> pdb=" O MET M 409 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 348 through 354 removed outlier: 6.586A pdb=" N VAL M 348 " --> pdb=" O LEU M 377 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU M 379 " --> pdb=" O VAL M 348 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET M 350 " --> pdb=" O LEU M 379 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU M 381 " --> pdb=" O MET M 350 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE M 352 " --> pdb=" O LEU M 381 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL M 383 " --> pdb=" O ILE M 352 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N TYR M 401 " --> pdb=" O SER M 376 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR M 378 " --> pdb=" O TYR M 401 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU M 476 " --> pdb=" O ARG M 400 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL M 402 " --> pdb=" O GLU M 476 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 29 through 32 removed outlier: 5.857A pdb=" N ILE N 60 " --> pdb=" O SER N 98 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL N 100 " --> pdb=" O ILE N 60 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N MET N 62 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET N 102 " --> pdb=" O MET N 62 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE N 64 " --> pdb=" O MET N 102 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU N 104 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER N 66 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL N 106 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU N 128 " --> pdb=" O ASN N 101 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLY N 103 " --> pdb=" O LEU N 128 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N MET N 130 " --> pdb=" O GLY N 103 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA N 105 " --> pdb=" O MET N 130 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE N 131 " --> pdb=" O LEU N 184 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 29 through 32 removed outlier: 5.857A pdb=" N ILE N 60 " --> pdb=" O SER N 98 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL N 100 " --> pdb=" O ILE N 60 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N MET N 62 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET N 102 " --> pdb=" O MET N 62 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE N 64 " --> pdb=" O MET N 102 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU N 104 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER N 66 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL N 106 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LYS N 122 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR N 99 " --> pdb=" O LYS N 122 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER N 123 " --> pdb=" O GLU N 199 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 37 through 38 Processing sheet with id=AD8, first strand: chain 'P' and resid 72 through 73 removed outlier: 3.717A pdb=" N VAL P 73 " --> pdb=" O ALA P 51 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA P 51 " --> pdb=" O VAL P 73 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS P 52 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU P 24 " --> pdb=" O GLY P 54 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL P 23 " --> pdb=" O VAL P 93 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL P 93 " --> pdb=" O VAL P 23 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE P 25 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE P 91 " --> pdb=" O ILE P 25 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY P 88 " --> pdb=" O VAL P 85 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 2 through 4 removed outlier: 6.720A pdb=" N ILE Q 3 " --> pdb=" O LYS Q 86 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN Q 83 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU Q 20 " --> pdb=" O VAL Q 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 103 through 104 Processing sheet with id=AE2, first strand: chain 'Q' and resid 181 through 184 removed outlier: 7.003A pdb=" N LEU Q 126 " --> pdb=" O VAL Q 156 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL Q 158 " --> pdb=" O ARG Q 124 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ARG Q 124 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS Q 199 " --> pdb=" O VAL Q 129 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 160 through 163 removed outlier: 3.994A pdb=" N LYS Q 162 " --> pdb=" O ARG Q 172 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 12 through 13 removed outlier: 3.501A pdb=" N LYS R 12 " --> pdb=" O GLN S 192 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 17 through 21 removed outlier: 3.894A pdb=" N THR R 71 " --> pdb=" O LEU R 82 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 62 through 65 removed outlier: 4.130A pdb=" N LYS R 62 " --> pdb=" O LEU R 92 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY R 90 " --> pdb=" O ILE R 64 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 163 through 164 removed outlier: 4.231A pdb=" N ALA R 140 " --> pdb=" O LEU R 109 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU R 109 " --> pdb=" O ALA R 140 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 145 through 146 Processing sheet with id=AE9, first strand: chain 'S' and resid 48 through 50 removed outlier: 6.124A pdb=" N ILE S 48 " --> pdb=" O LYS S 21 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS S 21 " --> pdb=" O ILE S 48 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA S 50 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR S 71 " --> pdb=" O LEU S 82 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 138 through 141 removed outlier: 3.572A pdb=" N VAL S 139 " --> pdb=" O LEU S 109 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU S 109 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR S 172 " --> pdb=" O VAL S 183 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.745A pdb=" N ALA S 152 " --> pdb=" O ASP S 147 " (cutoff:3.500A) 928 hydrogen bonds defined for protein. 2661 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: 5.18 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9212 1.35 - 1.46: 5924 1.46 - 1.58: 12720 1.58 - 1.70: 0 1.70 - 1.82: 293 Bond restraints: 28149 Sorted by residual: bond pdb=" CA THR O 35 " pdb=" CB THR O 35 " ideal model delta sigma weight residual 1.530 1.575 -0.045 1.57e-02 4.06e+03 8.32e+00 bond pdb=" N SER S 187 " pdb=" CA SER S 187 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.90e-02 2.77e+03 4.97e+00 bond pdb=" C PRO Q 37 " pdb=" N PRO Q 38 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.61e+00 bond pdb=" C GLU S 186 " pdb=" N SER S 187 " ideal model delta sigma weight residual 1.329 1.358 -0.029 1.40e-02 5.10e+03 4.25e+00 bond pdb=" C GLU R 186 " pdb=" N SER R 187 " ideal model delta sigma weight residual 1.329 1.358 -0.029 1.40e-02 5.10e+03 4.24e+00 ... (remaining 28144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 37853 3.48 - 6.96: 160 6.96 - 10.44: 24 10.44 - 13.92: 4 13.92 - 17.40: 2 Bond angle restraints: 38043 Sorted by residual: angle pdb=" C GLU R 186 " pdb=" N SER R 187 " pdb=" CA SER R 187 " ideal model delta sigma weight residual 121.70 139.10 -17.40 1.80e+00 3.09e-01 9.34e+01 angle pdb=" C GLU S 186 " pdb=" N SER S 187 " pdb=" CA SER S 187 " ideal model delta sigma weight residual 121.70 137.08 -15.38 1.80e+00 3.09e-01 7.30e+01 angle pdb=" C VAL R 33 " pdb=" N LEU R 34 " pdb=" CA LEU R 34 " ideal model delta sigma weight residual 121.54 131.41 -9.87 1.91e+00 2.74e-01 2.67e+01 angle pdb=" C LYS S 168 " pdb=" N TYR S 169 " pdb=" CA TYR S 169 " ideal model delta sigma weight residual 122.61 129.77 -7.16 1.56e+00 4.11e-01 2.11e+01 angle pdb=" C LYS P 86 " pdb=" N GLU P 87 " pdb=" CA GLU P 87 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 ... (remaining 38038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 15520 17.12 - 34.24: 1259 34.24 - 51.35: 303 51.35 - 68.47: 42 68.47 - 85.59: 16 Dihedral angle restraints: 17140 sinusoidal: 6868 harmonic: 10272 Sorted by residual: dihedral pdb=" CA GLU S 186 " pdb=" C GLU S 186 " pdb=" N SER S 187 " pdb=" CA SER S 187 " ideal model delta harmonic sigma weight residual 0.00 39.18 -39.18 0 5.00e+00 4.00e-02 6.14e+01 dihedral pdb=" CA GLU R 186 " pdb=" C GLU R 186 " pdb=" N SER R 187 " pdb=" CA SER R 187 " ideal model delta harmonic sigma weight residual 0.00 32.29 -32.29 0 5.00e+00 4.00e-02 4.17e+01 dihedral pdb=" CA LEU R 34 " pdb=" C LEU R 34 " pdb=" N LEU R 35 " pdb=" CA LEU R 35 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 17137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3298 0.049 - 0.098: 734 0.098 - 0.147: 230 0.147 - 0.195: 18 0.195 - 0.244: 7 Chirality restraints: 4287 Sorted by residual: chirality pdb=" CB VAL N 327 " pdb=" CA VAL N 327 " pdb=" CG1 VAL N 327 " pdb=" CG2 VAL N 327 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA LEU K 135 " pdb=" N LEU K 135 " pdb=" C LEU K 135 " pdb=" CB LEU K 135 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL S 123 " pdb=" CA VAL S 123 " pdb=" CG1 VAL S 123 " pdb=" CG2 VAL S 123 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 4284 not shown) Planarity restraints: 4940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 16 " -0.053 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO K 17 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO K 17 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO K 17 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 43 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.20e+00 pdb=" N PRO Q 44 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO Q 44 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO Q 44 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 118 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO F 119 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 119 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 119 " 0.031 5.00e-02 4.00e+02 ... (remaining 4937 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7712 2.80 - 3.33: 22795 3.33 - 3.85: 44561 3.85 - 4.38: 50569 4.38 - 4.90: 85203 Nonbonded interactions: 210840 Sorted by model distance: nonbonded pdb=" O THR M 464 " pdb=" OG1 THR M 468 " model vdw 2.280 3.040 nonbonded pdb=" O ASP I 27 " pdb=" OG SER I 30 " model vdw 2.285 3.040 nonbonded pdb=" O THR H 464 " pdb=" OG1 THR H 468 " model vdw 2.292 3.040 nonbonded pdb=" O PHE D 135 " pdb=" OG SER D 139 " model vdw 2.308 3.040 nonbonded pdb=" O ALA M 439 " pdb=" OG SER M 443 " model vdw 2.320 3.040 ... (remaining 210835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 54 through 225) selection = (chain 'D' and resid 54 through 225) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'E' selection = (chain 'G' and resid 17 through 190) } ncs_group { reference = (chain 'H' and resid 346 through 478) selection = (chain 'J' and resid 346 through 478) selection = chain 'M' } ncs_group { reference = chain 'R' selection = chain 'S' } 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.900 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 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 : 0.003 0.050 28149 Z= 0.152 Angle : 0.707 17.398 38043 Z= 0.386 Chirality : 0.046 0.244 4287 Planarity : 0.006 0.078 4940 Dihedral : 13.219 85.589 10566 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.14 % Allowed : 6.76 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -5.02 (0.10), residues: 3543 helix: -4.88 (0.04), residues: 1341 sheet: -0.91 (0.22), residues: 467 loop : -2.65 (0.11), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 204 TYR 0.011 0.001 TYR S 166 PHE 0.015 0.001 PHE P 92 TRP 0.009 0.001 TRP L 96 HIS 0.014 0.001 HIS O 113 Details of bonding type rmsd covalent geometry : bond 0.00283 (28149) covalent geometry : angle 0.70698 (38043) hydrogen bonds : bond 0.32382 ( 900) hydrogen bonds : angle 10.06693 ( 2661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1172 time to evaluate : 0.973 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: A 50 ASP cc_start: 0.7685 (p0) cc_final: 0.7484 (p0) REVERT: A 51 LYS cc_start: 0.8747 (tppt) cc_final: 0.8321 (tptp) REVERT: A 64 GLU cc_start: 0.7213 (tp30) cc_final: 0.6681 (tp30) REVERT: A 78 SER cc_start: 0.8823 (p) cc_final: 0.8592 (t) REVERT: A 156 ASN cc_start: 0.7982 (m110) cc_final: 0.7412 (t0) REVERT: A 164 ARG cc_start: 0.5721 (mtp180) cc_final: 0.5183 (mtp85) REVERT: A 172 MET cc_start: 0.5834 (ptm) cc_final: 0.5255 (ptm) REVERT: A 187 MET cc_start: 0.6502 (mpp) cc_final: 0.6120 (mtm) REVERT: A 214 ILE cc_start: 0.8689 (mm) cc_final: 0.8317 (mm) REVERT: B 76 LEU cc_start: 0.9194 (mm) cc_final: 0.8584 (mp) REVERT: B 167 THR cc_start: 0.7880 (p) cc_final: 0.7253 (m) REVERT: B 200 LYS cc_start: 0.8661 (tppt) cc_final: 0.8115 (tptt) REVERT: C 47 LEU cc_start: 0.8615 (mm) cc_final: 0.8214 (mm) REVERT: C 48 LEU cc_start: 0.8952 (mm) cc_final: 0.8480 (mm) REVERT: C 72 MET cc_start: 0.8326 (tpt) cc_final: 0.7763 (tpp) REVERT: C 74 ILE cc_start: 0.8961 (mt) cc_final: 0.7932 (mm) REVERT: C 159 LEU cc_start: 0.6835 (tp) cc_final: 0.6102 (pp) REVERT: C 165 ASP cc_start: 0.8159 (m-30) cc_final: 0.7636 (m-30) REVERT: C 167 ASP cc_start: 0.8640 (p0) cc_final: 0.8353 (p0) REVERT: C 175 LEU cc_start: 0.7935 (tp) cc_final: 0.6915 (tp) REVERT: C 180 TYR cc_start: 0.5015 (t80) cc_final: 0.4801 (t80) REVERT: D 165 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8000 (mt0) REVERT: D 168 ASP cc_start: 0.7850 (t0) cc_final: 0.7471 (t0) REVERT: E 34 GLU cc_start: 0.7318 (pt0) cc_final: 0.6981 (mm-30) REVERT: E 74 ILE cc_start: 0.8443 (mp) cc_final: 0.7690 (mp) REVERT: E 82 ARG cc_start: 0.7157 (ptt-90) cc_final: 0.6054 (ptt180) REVERT: E 84 ASP cc_start: 0.7168 (m-30) cc_final: 0.6954 (m-30) REVERT: E 164 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7753 (mm-30) REVERT: F 110 VAL cc_start: 0.9304 (m) cc_final: 0.9053 (t) REVERT: F 154 MET cc_start: 0.7365 (tmm) cc_final: 0.6384 (ttt) REVERT: F 195 MET cc_start: 0.7212 (tpt) cc_final: 0.6875 (tpp) REVERT: G 146 ASN cc_start: 0.7653 (t0) cc_final: 0.6951 (t0) REVERT: H 352 ILE cc_start: 0.8738 (mm) cc_final: 0.8520 (mt) REVERT: H 425 TRP cc_start: 0.8022 (t-100) cc_final: 0.7147 (t-100) REVERT: H 451 HIS cc_start: 0.7031 (p-80) cc_final: 0.6711 (p-80) REVERT: H 471 TYR cc_start: 0.7510 (t80) cc_final: 0.6724 (t80) REVERT: I 80 ILE cc_start: 0.8560 (mm) cc_final: 0.8179 (pt) REVERT: I 102 PHE cc_start: 0.3219 (t80) cc_final: 0.1392 (t80) REVERT: I 147 ASN cc_start: 0.8052 (p0) cc_final: 0.7659 (p0) REVERT: J 371 PHE cc_start: 0.5939 (p90) cc_final: 0.5678 (p90) REVERT: J 411 HIS cc_start: 0.7346 (t70) cc_final: 0.7140 (t70) REVERT: J 425 TRP cc_start: 0.7312 (t60) cc_final: 0.6977 (t-100) REVERT: J 429 GLN cc_start: 0.7918 (mm110) cc_final: 0.7631 (mm-40) REVERT: J 432 MET cc_start: 0.8200 (mmp) cc_final: 0.7207 (mmm) REVERT: J 436 LEU cc_start: 0.7094 (tt) cc_final: 0.6756 (mt) REVERT: K 64 ASN cc_start: 0.6728 (t0) cc_final: 0.6411 (t0) REVERT: K 150 ARG cc_start: 0.7376 (mtp180) cc_final: 0.7150 (ttm170) REVERT: K 215 MET cc_start: 0.5657 (ppp) cc_final: 0.4588 (mmm) REVERT: L 111 TYR cc_start: 0.7902 (t80) cc_final: 0.7448 (t80) REVERT: L 155 MET cc_start: 0.7566 (tpt) cc_final: 0.7236 (tpt) REVERT: L 169 GLU cc_start: 0.8060 (pp20) cc_final: 0.7558 (pt0) REVERT: L 200 ILE cc_start: 0.7637 (mm) cc_final: 0.7406 (tp) REVERT: M 414 GLU cc_start: 0.7784 (pp20) cc_final: 0.7414 (pm20) REVERT: M 417 LEU cc_start: 0.8658 (mp) cc_final: 0.7748 (mt) REVERT: M 420 GLN cc_start: 0.6786 (tm-30) cc_final: 0.6239 (tt0) REVERT: M 431 ILE cc_start: 0.8513 (mm) cc_final: 0.8137 (mm) REVERT: N 19 ASP cc_start: 0.7728 (p0) cc_final: 0.7330 (p0) REVERT: N 152 ARG cc_start: 0.7636 (mmt180) cc_final: 0.7367 (mmm-85) REVERT: N 160 GLU cc_start: 0.6774 (tp30) cc_final: 0.6116 (tp30) REVERT: N 180 MET cc_start: 0.7487 (ttp) cc_final: 0.7258 (ttp) REVERT: N 181 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7568 (mm-40) REVERT: N 185 TYR cc_start: 0.8388 (m-80) cc_final: 0.8011 (m-80) REVERT: N 291 ASN cc_start: 0.7691 (m-40) cc_final: 0.6746 (p0) REVERT: O 45 MET cc_start: 0.7829 (tpp) cc_final: 0.7618 (tpp) REVERT: P 40 LEU cc_start: 0.5782 (tp) cc_final: 0.5290 (tp) REVERT: Q 85 LEU cc_start: 0.6181 (tp) cc_final: 0.5507 (tp) REVERT: Q 163 TYR cc_start: 0.2441 (t80) cc_final: 0.1965 (t80) REVERT: R 166 TYR cc_start: 0.4770 (p90) cc_final: 0.4441 (p90) REVERT: S 19 LEU cc_start: 0.4559 (tp) cc_final: 0.4335 (tp) REVERT: S 180 ASN cc_start: 0.5540 (p0) cc_final: 0.5294 (p0) outliers start: 4 outliers final: 0 residues processed: 1176 average time/residue: 0.1863 time to fit residues: 334.9212 Evaluate side-chains 711 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 711 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 GLN A 136 GLN A 156 ASN A 176 GLN A 191 GLN A 217 GLN B 59 GLN B 89 ASN ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 174 ASN B 178 HIS C 51 GLN C 146 ASN C 148 ASN C 185 HIS D 172 GLN E 44 GLN ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 60 GLN F 116 HIS F 150 ASN F 156 HIS F 157 GLN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 HIS G 44 GLN G 136 GLN G 146 ASN ** H 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 491 ASN I 55 GLN ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN J 361 ASN ** J 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 420 GLN ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 GLN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 GLN K 230 GLN L 98 ASN L 115 GLN L 151 HIS ** L 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 ASN ** M 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN N 133 GLN ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 HIS ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.106340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.096606 restraints weight = 101893.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.098396 restraints weight = 55253.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.099593 restraints weight = 33745.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.100397 restraints weight = 22747.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.101009 restraints weight = 16662.320| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 28149 Z= 0.267 Angle : 0.801 14.765 38043 Z= 0.417 Chirality : 0.048 0.268 4287 Planarity : 0.006 0.080 4940 Dihedral : 5.015 49.461 3885 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 3.51 % Allowed : 15.95 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.12 (0.12), residues: 3543 helix: -2.52 (0.10), residues: 1399 sheet: -0.56 (0.23), residues: 494 loop : -2.05 (0.13), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 107 TYR 0.030 0.002 TYR K 163 PHE 0.025 0.002 PHE S 174 TRP 0.024 0.002 TRP O 112 HIS 0.010 0.003 HIS F 116 Details of bonding type rmsd covalent geometry : bond 0.00566 (28149) covalent geometry : angle 0.80120 (38043) hydrogen bonds : bond 0.04239 ( 900) hydrogen bonds : angle 5.16233 ( 2661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 775 time to evaluate : 1.000 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: A 51 LYS cc_start: 0.8756 (tppt) cc_final: 0.8525 (tptt) REVERT: A 136 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8081 (mt0) REVERT: A 174 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: A 176 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8135 (pm20) REVERT: B 104 VAL cc_start: 0.9295 (OUTLIER) cc_final: 0.9005 (t) REVERT: C 23 ARG cc_start: 0.8587 (mtm110) cc_final: 0.8333 (mtm180) REVERT: C 74 ILE cc_start: 0.8848 (mt) cc_final: 0.8554 (mt) REVERT: C 127 SER cc_start: 0.8633 (t) cc_final: 0.8319 (p) REVERT: C 144 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8269 (mtmm) REVERT: C 164 GLU cc_start: 0.7963 (pt0) cc_final: 0.7485 (pt0) REVERT: D 83 TYR cc_start: 0.8329 (t80) cc_final: 0.7684 (t80) REVERT: D 96 TYR cc_start: 0.7846 (t80) cc_final: 0.6517 (t80) REVERT: D 122 SER cc_start: 0.8283 (p) cc_final: 0.8048 (m) REVERT: D 124 CYS cc_start: 0.8613 (t) cc_final: 0.8411 (t) REVERT: E 34 GLU cc_start: 0.7301 (pt0) cc_final: 0.7003 (mm-30) REVERT: E 44 GLN cc_start: 0.8691 (pt0) cc_final: 0.8393 (pt0) REVERT: E 96 MET cc_start: 0.8341 (mmm) cc_final: 0.8129 (mmm) REVERT: E 165 ASP cc_start: 0.7233 (m-30) cc_final: 0.6991 (m-30) REVERT: F 64 ARG cc_start: 0.7746 (ttt-90) cc_final: 0.7496 (ttt-90) REVERT: F 83 TYR cc_start: 0.7448 (t80) cc_final: 0.7246 (t80) REVERT: F 154 MET cc_start: 0.7487 (tmm) cc_final: 0.7015 (ttt) REVERT: F 203 ASP cc_start: 0.7903 (p0) cc_final: 0.7689 (p0) REVERT: F 204 ARG cc_start: 0.7318 (pmt-80) cc_final: 0.7072 (pmt-80) REVERT: G 138 LYS cc_start: 0.8595 (ptmm) cc_final: 0.8244 (ptmm) REVERT: H 352 ILE cc_start: 0.9126 (mm) cc_final: 0.8841 (mt) REVERT: H 420 GLN cc_start: 0.8485 (mt0) cc_final: 0.8082 (mt0) REVERT: H 430 GLU cc_start: 0.7003 (tp30) cc_final: 0.6660 (tp30) REVERT: H 470 TYR cc_start: 0.7577 (t80) cc_final: 0.7314 (t80) REVERT: I 74 LEU cc_start: 0.8903 (pp) cc_final: 0.8540 (pp) REVERT: K 215 MET cc_start: 0.5745 (ppp) cc_final: 0.4763 (mmm) REVERT: L 73 ASP cc_start: 0.7280 (p0) cc_final: 0.6868 (p0) REVERT: L 169 GLU cc_start: 0.7465 (pp20) cc_final: 0.6646 (pp20) REVERT: L 173 GLU cc_start: 0.6547 (pt0) cc_final: 0.5432 (pt0) REVERT: M 420 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6640 (tt0) REVERT: M 456 ASP cc_start: 0.8487 (t0) cc_final: 0.8030 (t0) REVERT: M 476 GLU cc_start: 0.7556 (pm20) cc_final: 0.7303 (pm20) REVERT: N 19 ASP cc_start: 0.8166 (p0) cc_final: 0.7783 (p0) REVERT: N 64 ILE cc_start: 0.9139 (mm) cc_final: 0.8906 (mt) REVERT: N 109 SER cc_start: 0.8818 (m) cc_final: 0.8470 (p) REVERT: N 115 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8545 (m-80) REVERT: N 122 LYS cc_start: 0.8032 (mttt) cc_final: 0.7719 (mtmt) REVERT: N 151 TRP cc_start: 0.8709 (t-100) cc_final: 0.8445 (t-100) REVERT: N 186 MET cc_start: 0.8034 (mmm) cc_final: 0.7795 (mtt) REVERT: O 97 ASP cc_start: 0.7243 (t70) cc_final: 0.6911 (t0) REVERT: P 72 MET cc_start: 0.5787 (tmm) cc_final: 0.5576 (tmm) REVERT: Q 51 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6971 (mm-40) REVERT: Q 97 ARG cc_start: 0.5971 (mtp180) cc_final: 0.5249 (mmt-90) REVERT: Q 163 TYR cc_start: 0.2378 (t80) cc_final: 0.1776 (t80) REVERT: R 12 LYS cc_start: 0.5784 (tptt) cc_final: 0.5460 (tptp) REVERT: R 165 MET cc_start: 0.7011 (mmm) cc_final: 0.6780 (tpp) REVERT: R 166 TYR cc_start: 0.5356 (p90) cc_final: 0.5067 (p90) REVERT: S 109 LEU cc_start: 0.4599 (OUTLIER) cc_final: 0.4348 (pp) REVERT: S 159 THR cc_start: 0.5104 (m) cc_final: 0.4698 (p) REVERT: S 180 ASN cc_start: 0.6112 (p0) cc_final: 0.5600 (p0) REVERT: S 190 LEU cc_start: 0.7495 (mt) cc_final: 0.7272 (mt) outliers start: 104 outliers final: 51 residues processed: 843 average time/residue: 0.1740 time to fit residues: 228.7603 Evaluate side-chains 698 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 639 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 494 TRP Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 406 CYS Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 247 ARG Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 190 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 128 GLU Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 281 optimal weight: 0.9980 chunk 262 optimal weight: 10.0000 chunk 272 optimal weight: 8.9990 chunk 279 optimal weight: 8.9990 chunk 306 optimal weight: 5.9990 chunk 314 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 333 optimal weight: 0.0570 chunk 277 optimal weight: 0.4980 overall best weight: 2.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN A 176 GLN B 56 GLN B 75 ASN C 51 GLN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS D 141 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 451 HIS ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN ** J 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 HIS ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 GLN K 230 GLN L 90 GLN ** L 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.104335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.094619 restraints weight = 100996.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.096399 restraints weight = 54081.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.097574 restraints weight = 32992.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.098413 restraints weight = 22348.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.099001 restraints weight = 16146.358| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 28149 Z= 0.182 Angle : 0.681 14.470 38043 Z= 0.346 Chirality : 0.046 0.242 4287 Planarity : 0.004 0.046 4940 Dihedral : 4.780 35.088 3885 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.65 % Allowed : 19.39 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -2.19 (0.13), residues: 3543 helix: -1.29 (0.12), residues: 1400 sheet: -0.49 (0.23), residues: 499 loop : -1.85 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 145 TYR 0.021 0.002 TYR C 142 PHE 0.022 0.002 PHE S 174 TRP 0.010 0.002 TRP M 425 HIS 0.010 0.002 HIS L 171 Details of bonding type rmsd covalent geometry : bond 0.00417 (28149) covalent geometry : angle 0.68064 (38043) hydrogen bonds : bond 0.03858 ( 900) hydrogen bonds : angle 4.77754 ( 2661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 708 time to evaluate : 0.765 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: A 51 LYS cc_start: 0.8762 (tppt) cc_final: 0.8551 (tptt) REVERT: A 176 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8016 (pm20) REVERT: C 51 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8141 (mt0) REVERT: C 127 SER cc_start: 0.8661 (t) cc_final: 0.8387 (p) REVERT: C 142 TYR cc_start: 0.8295 (t80) cc_final: 0.8057 (t80) REVERT: C 144 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8060 (mtmm) REVERT: C 146 ASN cc_start: 0.8421 (m-40) cc_final: 0.8163 (m110) REVERT: C 167 ASP cc_start: 0.8441 (p0) cc_final: 0.8088 (p0) REVERT: C 171 TYR cc_start: 0.8020 (m-80) cc_final: 0.7683 (m-80) REVERT: D 83 TYR cc_start: 0.8443 (t80) cc_final: 0.7773 (t80) REVERT: D 96 TYR cc_start: 0.7894 (t80) cc_final: 0.6950 (t80) REVERT: D 128 LEU cc_start: 0.8665 (tp) cc_final: 0.8355 (tp) REVERT: E 32 GLU cc_start: 0.7354 (tp30) cc_final: 0.6980 (tp30) REVERT: E 118 MET cc_start: 0.7849 (tpt) cc_final: 0.7619 (tpt) REVERT: F 154 MET cc_start: 0.7552 (tmm) cc_final: 0.6992 (ttt) REVERT: G 138 LYS cc_start: 0.8534 (ptmm) cc_final: 0.8266 (ptmm) REVERT: G 139 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7941 (tm-30) REVERT: H 378 THR cc_start: 0.9531 (t) cc_final: 0.9202 (m) REVERT: H 430 GLU cc_start: 0.7197 (tp30) cc_final: 0.6483 (tp30) REVERT: H 447 TYR cc_start: 0.8642 (m-80) cc_final: 0.7933 (m-80) REVERT: H 470 TYR cc_start: 0.7596 (t80) cc_final: 0.7376 (t80) REVERT: I 74 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8593 (pp) REVERT: I 192 ARG cc_start: 0.6951 (ptt-90) cc_final: 0.6646 (ptp90) REVERT: J 399 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7080 (mm-30) REVERT: J 429 GLN cc_start: 0.7975 (mm110) cc_final: 0.7768 (mm-40) REVERT: K 191 VAL cc_start: 0.7200 (m) cc_final: 0.6870 (p) REVERT: K 215 MET cc_start: 0.5532 (ppp) cc_final: 0.4870 (mmm) REVERT: L 62 LYS cc_start: 0.8034 (tttt) cc_final: 0.7558 (tttt) REVERT: L 73 ASP cc_start: 0.7372 (p0) cc_final: 0.6892 (p0) REVERT: L 169 GLU cc_start: 0.7365 (pp20) cc_final: 0.6484 (pp20) REVERT: L 173 GLU cc_start: 0.6286 (pt0) cc_final: 0.5108 (pt0) REVERT: M 420 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: M 456 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8191 (t0) REVERT: N 19 ASP cc_start: 0.8089 (p0) cc_final: 0.7640 (p0) REVERT: N 25 PHE cc_start: 0.8103 (t80) cc_final: 0.7838 (t80) REVERT: N 47 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7572 (mm-30) REVERT: N 122 LYS cc_start: 0.7930 (mttt) cc_final: 0.7584 (mtmt) REVERT: O 97 ASP cc_start: 0.7251 (t70) cc_final: 0.6998 (t0) REVERT: P 72 MET cc_start: 0.5501 (tmm) cc_final: 0.5041 (tmm) REVERT: P 73 VAL cc_start: 0.7176 (t) cc_final: 0.6786 (t) REVERT: Q 1 GLU cc_start: 0.5756 (OUTLIER) cc_final: 0.5544 (pt0) REVERT: Q 51 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6920 (mm-40) REVERT: Q 97 ARG cc_start: 0.5778 (mtp180) cc_final: 0.5289 (mmt-90) REVERT: Q 163 TYR cc_start: 0.2533 (t80) cc_final: 0.1649 (t80) REVERT: R 165 MET cc_start: 0.7009 (mmm) cc_final: 0.6374 (tpp) REVERT: S 19 LEU cc_start: 0.5627 (tp) cc_final: 0.5316 (tp) REVERT: S 109 LEU cc_start: 0.4770 (OUTLIER) cc_final: 0.4521 (pp) REVERT: S 159 THR cc_start: 0.5224 (m) cc_final: 0.4812 (p) REVERT: S 180 ASN cc_start: 0.6189 (p0) cc_final: 0.5640 (p0) outliers start: 108 outliers final: 68 residues processed: 775 average time/residue: 0.1613 time to fit residues: 199.3807 Evaluate side-chains 723 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 647 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 165 TYR Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 434 ILE Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 209 PHE Chi-restraints excluded: chain M residue 364 THR Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain M residue 456 ASP Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 247 ARG Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 48 ASN Chi-restraints excluded: chain Q residue 1 GLU Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 255 optimal weight: 3.9990 chunk 204 optimal weight: 0.0870 chunk 85 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 290 optimal weight: 0.0870 chunk 307 optimal weight: 0.2980 chunk 279 optimal weight: 9.9990 chunk 236 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 0.5980 chunk 291 optimal weight: 5.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN B 75 ASN C 24 GLN D 75 ASN F 150 ASN F 184 ASN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 451 HIS J 366 HIS ** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 157 HIS ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.106406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.096539 restraints weight = 100706.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.098356 restraints weight = 53709.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.099539 restraints weight = 32543.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.100373 restraints weight = 21934.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.100977 restraints weight = 15915.794| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28149 Z= 0.116 Angle : 0.628 13.857 38043 Z= 0.311 Chirality : 0.044 0.184 4287 Planarity : 0.004 0.064 4940 Dihedral : 4.528 37.200 3885 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.11 % Allowed : 21.18 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.70 (0.13), residues: 3543 helix: -0.68 (0.13), residues: 1393 sheet: -0.57 (0.23), residues: 493 loop : -1.63 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 73 TYR 0.018 0.001 TYR C 171 PHE 0.028 0.001 PHE N 92 TRP 0.013 0.001 TRP J 425 HIS 0.010 0.001 HIS K 5 Details of bonding type rmsd covalent geometry : bond 0.00268 (28149) covalent geometry : angle 0.62752 (38043) hydrogen bonds : bond 0.03299 ( 900) hydrogen bonds : angle 4.52799 ( 2661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 708 time to evaluate : 0.902 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: A 51 LYS cc_start: 0.8749 (tppt) cc_final: 0.8522 (tptt) REVERT: A 176 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: A 203 ARG cc_start: 0.7532 (mtt-85) cc_final: 0.7145 (mtt-85) REVERT: C 23 ARG cc_start: 0.8352 (mtm110) cc_final: 0.8109 (mtm180) REVERT: C 134 GLU cc_start: 0.7324 (tp30) cc_final: 0.6934 (tp30) REVERT: C 142 TYR cc_start: 0.8269 (t80) cc_final: 0.8000 (t80) REVERT: C 144 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.7994 (mtmm) REVERT: C 146 ASN cc_start: 0.8435 (m-40) cc_final: 0.8199 (m110) REVERT: D 83 TYR cc_start: 0.8429 (t80) cc_final: 0.7719 (t80) REVERT: D 90 LYS cc_start: 0.8528 (mmmt) cc_final: 0.8327 (mmmt) REVERT: D 96 TYR cc_start: 0.7986 (t80) cc_final: 0.6807 (t80) REVERT: D 128 LEU cc_start: 0.8712 (tp) cc_final: 0.8390 (tp) REVERT: D 184 ASN cc_start: 0.8784 (m-40) cc_final: 0.8453 (m-40) REVERT: E 111 SER cc_start: 0.6972 (t) cc_final: 0.6444 (t) REVERT: F 64 ARG cc_start: 0.7525 (ttt-90) cc_final: 0.7295 (ttt-90) REVERT: F 89 ASN cc_start: 0.7637 (m-40) cc_final: 0.7411 (m-40) REVERT: F 154 MET cc_start: 0.7520 (tmm) cc_final: 0.6803 (ttt) REVERT: F 204 ARG cc_start: 0.7626 (pmt-80) cc_final: 0.6788 (tpp80) REVERT: G 138 LYS cc_start: 0.8506 (ptmm) cc_final: 0.8239 (ptmm) REVERT: G 139 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8095 (tm-30) REVERT: H 378 THR cc_start: 0.9491 (t) cc_final: 0.9220 (m) REVERT: H 430 GLU cc_start: 0.7138 (tp30) cc_final: 0.6419 (tp30) REVERT: H 447 TYR cc_start: 0.8589 (m-80) cc_final: 0.7843 (m-80) REVERT: H 470 TYR cc_start: 0.7459 (t80) cc_final: 0.7254 (t80) REVERT: I 74 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8535 (pp) REVERT: I 114 LYS cc_start: 0.8677 (ptmt) cc_final: 0.8458 (ptmm) REVERT: I 192 ARG cc_start: 0.6909 (ptt-90) cc_final: 0.6620 (ptp90) REVERT: J 429 GLN cc_start: 0.8061 (mm110) cc_final: 0.7483 (mm-40) REVERT: K 49 PHE cc_start: 0.8456 (m-10) cc_final: 0.8180 (m-10) REVERT: K 191 VAL cc_start: 0.7024 (OUTLIER) cc_final: 0.6730 (p) REVERT: K 215 MET cc_start: 0.5500 (ppp) cc_final: 0.4834 (mmm) REVERT: L 54 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8153 (tp) REVERT: L 79 ILE cc_start: 0.8940 (pt) cc_final: 0.8599 (mt) REVERT: L 169 GLU cc_start: 0.7608 (pp20) cc_final: 0.7138 (pp20) REVERT: L 173 GLU cc_start: 0.6305 (pt0) cc_final: 0.5129 (pt0) REVERT: M 420 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: M 456 ASP cc_start: 0.8625 (t0) cc_final: 0.8235 (t0) REVERT: N 19 ASP cc_start: 0.8028 (p0) cc_final: 0.7720 (p0) REVERT: N 47 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7266 (mm-30) REVERT: O 34 GLU cc_start: 0.6913 (mp0) cc_final: 0.6610 (mp0) REVERT: O 97 ASP cc_start: 0.7198 (t70) cc_final: 0.6932 (t0) REVERT: O 136 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7819 (mm) REVERT: Q 51 GLN cc_start: 0.7212 (mm-40) cc_final: 0.6993 (mm-40) REVERT: Q 97 ARG cc_start: 0.5818 (mtp180) cc_final: 0.5401 (mmt-90) REVERT: Q 163 TYR cc_start: 0.2341 (t80) cc_final: 0.1363 (t80) REVERT: R 8 PHE cc_start: 0.4854 (OUTLIER) cc_final: 0.4424 (m-80) REVERT: R 12 LYS cc_start: 0.5721 (tptt) cc_final: 0.5480 (tptt) REVERT: R 39 VAL cc_start: -0.1946 (OUTLIER) cc_final: -0.2279 (m) REVERT: R 165 MET cc_start: 0.6967 (mmm) cc_final: 0.6425 (tpp) REVERT: R 166 TYR cc_start: 0.5409 (p90) cc_final: 0.5109 (p90) REVERT: S 19 LEU cc_start: 0.5651 (tp) cc_final: 0.5330 (tp) REVERT: S 109 LEU cc_start: 0.4877 (OUTLIER) cc_final: 0.4563 (pp) REVERT: S 159 THR cc_start: 0.5032 (m) cc_final: 0.4642 (p) REVERT: S 180 ASN cc_start: 0.6168 (p0) cc_final: 0.5706 (p0) outliers start: 92 outliers final: 50 residues processed: 765 average time/residue: 0.1677 time to fit residues: 203.7772 Evaluate side-chains 704 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 644 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 165 TYR Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 47 GLN Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 209 PHE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 364 THR Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain R residue 8 PHE Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 173 optimal weight: 8.9990 chunk 250 optimal weight: 0.0570 chunk 201 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 77 optimal weight: 0.1980 chunk 279 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 313 optimal weight: 0.7980 chunk 272 optimal weight: 0.6980 chunk 209 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 176 GLN B 75 ASN ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 ASN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 451 HIS ** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 HIS ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 GLN L 98 ASN ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.106945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.097120 restraints weight = 100411.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.098934 restraints weight = 53639.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.100124 restraints weight = 32466.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.100904 restraints weight = 21829.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.101511 restraints weight = 16060.600| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28149 Z= 0.111 Angle : 0.624 13.808 38043 Z= 0.307 Chirality : 0.044 0.363 4287 Planarity : 0.004 0.063 4940 Dihedral : 4.404 36.510 3885 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.84 % Allowed : 22.40 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.35 (0.14), residues: 3543 helix: -0.32 (0.14), residues: 1409 sheet: -0.44 (0.24), residues: 476 loop : -1.49 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 73 TYR 0.018 0.001 TYR H 462 PHE 0.025 0.001 PHE K 61 TRP 0.013 0.001 TRP L 208 HIS 0.005 0.001 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00259 (28149) covalent geometry : angle 0.62402 (38043) hydrogen bonds : bond 0.03110 ( 900) hydrogen bonds : angle 4.36332 ( 2661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 694 time to evaluate : 0.995 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: A 50 ASP cc_start: 0.7745 (p0) cc_final: 0.7535 (p0) REVERT: A 51 LYS cc_start: 0.8770 (tppt) cc_final: 0.8503 (tptt) REVERT: A 203 ARG cc_start: 0.7561 (mtt-85) cc_final: 0.7250 (mtt90) REVERT: C 32 GLU cc_start: 0.6665 (tm-30) cc_final: 0.5625 (tm-30) REVERT: C 34 GLU cc_start: 0.6765 (mp0) cc_final: 0.5643 (mp0) REVERT: C 121 GLN cc_start: 0.8266 (pt0) cc_final: 0.7175 (pt0) REVERT: C 134 GLU cc_start: 0.7336 (tp30) cc_final: 0.6971 (tp30) REVERT: C 142 TYR cc_start: 0.8327 (t80) cc_final: 0.8005 (t80) REVERT: C 146 ASN cc_start: 0.8530 (m-40) cc_final: 0.8276 (m110) REVERT: C 167 ASP cc_start: 0.8286 (p0) cc_final: 0.8053 (p0) REVERT: D 83 TYR cc_start: 0.8460 (t80) cc_final: 0.8074 (t80) REVERT: D 96 TYR cc_start: 0.7763 (t80) cc_final: 0.6771 (t80) REVERT: D 128 LEU cc_start: 0.8736 (tp) cc_final: 0.8435 (tp) REVERT: D 184 ASN cc_start: 0.8808 (m-40) cc_final: 0.8530 (m-40) REVERT: E 100 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9148 (mt) REVERT: E 111 SER cc_start: 0.6876 (t) cc_final: 0.6367 (t) REVERT: E 141 MET cc_start: 0.8336 (tpp) cc_final: 0.7692 (mmt) REVERT: F 154 MET cc_start: 0.7562 (tmm) cc_final: 0.6904 (ttt) REVERT: F 195 MET cc_start: 0.7553 (mmm) cc_final: 0.7107 (mmm) REVERT: G 138 LYS cc_start: 0.8503 (ptmm) cc_final: 0.8293 (ptmm) REVERT: H 378 THR cc_start: 0.9462 (t) cc_final: 0.9245 (m) REVERT: H 430 GLU cc_start: 0.7181 (tp30) cc_final: 0.6440 (tp30) REVERT: H 447 TYR cc_start: 0.8558 (m-80) cc_final: 0.7716 (m-80) REVERT: I 74 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8525 (pp) REVERT: I 114 LYS cc_start: 0.8704 (ptmt) cc_final: 0.8435 (ptmm) REVERT: I 192 ARG cc_start: 0.6939 (ptt-90) cc_final: 0.6636 (ptp90) REVERT: J 429 GLN cc_start: 0.7802 (mm110) cc_final: 0.7569 (mm-40) REVERT: K 49 PHE cc_start: 0.8562 (m-10) cc_final: 0.8323 (m-10) REVERT: K 191 VAL cc_start: 0.7056 (OUTLIER) cc_final: 0.6782 (p) REVERT: K 215 MET cc_start: 0.5536 (ppp) cc_final: 0.4890 (mmm) REVERT: L 54 LEU cc_start: 0.8542 (tt) cc_final: 0.8316 (tp) REVERT: L 79 ILE cc_start: 0.8946 (pt) cc_final: 0.8679 (mt) REVERT: L 169 GLU cc_start: 0.7610 (pp20) cc_final: 0.7222 (pp20) REVERT: L 173 GLU cc_start: 0.6556 (pt0) cc_final: 0.5404 (pt0) REVERT: M 420 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6914 (tt0) REVERT: M 430 GLU cc_start: 0.7446 (tp30) cc_final: 0.7205 (tp30) REVERT: M 456 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8294 (t0) REVERT: N 19 ASP cc_start: 0.8029 (p0) cc_final: 0.7778 (p0) REVERT: N 99 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8796 (p) REVERT: O 45 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7637 (tpp) REVERT: O 97 ASP cc_start: 0.7048 (t70) cc_final: 0.6820 (t0) REVERT: O 136 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7864 (mm) REVERT: P 72 MET cc_start: 0.4977 (tmm) cc_final: 0.4314 (tmm) REVERT: Q 97 ARG cc_start: 0.5799 (mtp180) cc_final: 0.5373 (mmt-90) REVERT: Q 163 TYR cc_start: 0.2316 (t80) cc_final: 0.1318 (t80) REVERT: R 8 PHE cc_start: 0.4955 (OUTLIER) cc_final: 0.4560 (m-80) REVERT: R 39 VAL cc_start: -0.1883 (OUTLIER) cc_final: -0.2299 (m) REVERT: R 165 MET cc_start: 0.7164 (mmm) cc_final: 0.6820 (tpp) REVERT: S 19 LEU cc_start: 0.5763 (tp) cc_final: 0.5442 (tp) REVERT: S 159 THR cc_start: 0.5190 (m) cc_final: 0.4762 (p) REVERT: S 180 ASN cc_start: 0.6116 (p0) cc_final: 0.5717 (p0) outliers start: 84 outliers final: 53 residues processed: 747 average time/residue: 0.1702 time to fit residues: 200.8448 Evaluate side-chains 703 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 640 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 165 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain J residue 364 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 209 PHE Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain M residue 364 THR Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain M residue 456 ASP Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain R residue 8 PHE Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 291 optimal weight: 0.9990 chunk 330 optimal weight: 0.9990 chunk 198 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 293 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 324 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 314 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 176 GLN B 56 GLN B 59 GLN B 75 ASN E 44 GLN ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN F 150 ASN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 451 HIS ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 HIS ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 GLN N 143 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.104608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.095015 restraints weight = 100097.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.096774 restraints weight = 52920.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.097931 restraints weight = 31967.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.098675 restraints weight = 21455.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.099286 restraints weight = 15772.805| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28149 Z= 0.137 Angle : 0.643 13.892 38043 Z= 0.319 Chirality : 0.045 0.241 4287 Planarity : 0.004 0.044 4940 Dihedral : 4.481 32.868 3885 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.31 % Allowed : 22.13 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.18 (0.14), residues: 3543 helix: -0.13 (0.14), residues: 1409 sheet: -0.31 (0.23), residues: 525 loop : -1.49 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 17 TYR 0.019 0.001 TYR C 171 PHE 0.033 0.001 PHE N 92 TRP 0.013 0.001 TRP L 55 HIS 0.024 0.002 HIS K 5 Details of bonding type rmsd covalent geometry : bond 0.00322 (28149) covalent geometry : angle 0.64277 (38043) hydrogen bonds : bond 0.03107 ( 900) hydrogen bonds : angle 4.34224 ( 2661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 668 time to evaluate : 0.967 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: A 51 LYS cc_start: 0.8804 (tppt) cc_final: 0.8531 (tptt) REVERT: A 203 ARG cc_start: 0.7664 (mtt-85) cc_final: 0.7338 (mtt90) REVERT: B 104 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.9019 (t) REVERT: B 154 MET cc_start: 0.7597 (tmm) cc_final: 0.7321 (ttm) REVERT: C 32 GLU cc_start: 0.6566 (tm-30) cc_final: 0.6138 (tm-30) REVERT: C 134 GLU cc_start: 0.7384 (tp30) cc_final: 0.6959 (tp30) REVERT: C 142 TYR cc_start: 0.8501 (t80) cc_final: 0.8130 (t80) REVERT: C 146 ASN cc_start: 0.8601 (m-40) cc_final: 0.8290 (m110) REVERT: C 164 GLU cc_start: 0.7463 (pp20) cc_final: 0.6701 (pp20) REVERT: C 167 ASP cc_start: 0.8336 (p0) cc_final: 0.8135 (p0) REVERT: D 83 TYR cc_start: 0.8566 (t80) cc_final: 0.8216 (t80) REVERT: D 96 TYR cc_start: 0.7827 (t80) cc_final: 0.6703 (t80) REVERT: D 128 LEU cc_start: 0.8745 (tp) cc_final: 0.8482 (tp) REVERT: E 88 TYR cc_start: 0.8687 (m-80) cc_final: 0.8195 (m-80) REVERT: E 100 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9138 (mt) REVERT: E 111 SER cc_start: 0.7242 (t) cc_final: 0.6802 (t) REVERT: F 64 ARG cc_start: 0.7591 (ttt-90) cc_final: 0.7304 (ttt-90) REVERT: F 154 MET cc_start: 0.7923 (tmm) cc_final: 0.7261 (ttt) REVERT: F 195 MET cc_start: 0.7571 (mmm) cc_final: 0.7190 (mmm) REVERT: G 139 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8085 (tm-30) REVERT: H 378 THR cc_start: 0.9485 (t) cc_final: 0.9250 (m) REVERT: H 430 GLU cc_start: 0.7381 (tp30) cc_final: 0.6392 (tp30) REVERT: H 447 TYR cc_start: 0.8551 (m-80) cc_final: 0.7636 (m-80) REVERT: I 74 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8524 (pp) REVERT: I 88 SER cc_start: 0.8813 (t) cc_final: 0.8266 (m) REVERT: I 91 ASN cc_start: 0.8135 (p0) cc_final: 0.7901 (p0) REVERT: I 114 LYS cc_start: 0.8739 (ptmt) cc_final: 0.8392 (ptmm) REVERT: I 192 ARG cc_start: 0.7090 (ptt-90) cc_final: 0.6691 (ptp90) REVERT: J 429 GLN cc_start: 0.7992 (mm110) cc_final: 0.7673 (mm-40) REVERT: J 467 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7526 (mt-10) REVERT: K 49 PHE cc_start: 0.8577 (m-10) cc_final: 0.8283 (m-10) REVERT: K 215 MET cc_start: 0.5739 (ppp) cc_final: 0.5146 (mmm) REVERT: L 54 LEU cc_start: 0.8632 (tt) cc_final: 0.8419 (tp) REVERT: L 79 ILE cc_start: 0.9058 (pt) cc_final: 0.8753 (mt) REVERT: L 169 GLU cc_start: 0.7712 (pp20) cc_final: 0.7445 (pp20) REVERT: M 420 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.7045 (tt0) REVERT: N 19 ASP cc_start: 0.8060 (p0) cc_final: 0.7826 (p0) REVERT: N 106 VAL cc_start: 0.8403 (t) cc_final: 0.8188 (t) REVERT: N 146 GLU cc_start: 0.7008 (pp20) cc_final: 0.6763 (pp20) REVERT: N 199 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7477 (pm20) REVERT: O 34 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6966 (mp0) REVERT: O 97 ASP cc_start: 0.7204 (t70) cc_final: 0.6923 (t0) REVERT: O 136 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8372 (mm) REVERT: P 72 MET cc_start: 0.5076 (tmm) cc_final: 0.4402 (tmm) REVERT: Q 163 TYR cc_start: 0.2519 (t80) cc_final: 0.1595 (t80) REVERT: R 39 VAL cc_start: -0.1736 (OUTLIER) cc_final: -0.2122 (m) REVERT: R 165 MET cc_start: 0.7034 (mmm) cc_final: 0.6576 (tpp) REVERT: R 166 TYR cc_start: 0.5714 (p90) cc_final: 0.5374 (p90) REVERT: S 159 THR cc_start: 0.5192 (m) cc_final: 0.4749 (p) REVERT: S 180 ASN cc_start: 0.6323 (p0) cc_final: 0.5834 (p0) outliers start: 98 outliers final: 59 residues processed: 736 average time/residue: 0.1643 time to fit residues: 192.7362 Evaluate side-chains 690 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 624 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 114 MET Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 209 PHE Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain M residue 364 THR Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 40 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 166 optimal weight: 0.3980 chunk 284 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 171 optimal weight: 0.6980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN C 44 GLN C 51 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 ASN G 44 GLN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN ** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 GLN ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.101870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.092435 restraints weight = 100952.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.094188 restraints weight = 53193.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.095336 restraints weight = 32148.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.096130 restraints weight = 21512.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.096533 restraints weight = 15520.626| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 28149 Z= 0.176 Angle : 0.700 14.168 38043 Z= 0.350 Chirality : 0.046 0.170 4287 Planarity : 0.004 0.045 4940 Dihedral : 4.810 36.216 3885 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.82 % Allowed : 22.87 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 3543 helix: -0.14 (0.14), residues: 1429 sheet: -0.42 (0.23), residues: 522 loop : -1.49 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 142 TYR 0.027 0.002 TYR C 171 PHE 0.033 0.002 PHE I 93 TRP 0.016 0.002 TRP L 55 HIS 0.006 0.002 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00409 (28149) covalent geometry : angle 0.70016 (38043) hydrogen bonds : bond 0.03356 ( 900) hydrogen bonds : angle 4.42381 ( 2661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 662 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9094 (t) REVERT: C 23 ARG cc_start: 0.8297 (mtm110) cc_final: 0.8094 (mtm110) REVERT: C 32 GLU cc_start: 0.6643 (tm-30) cc_final: 0.6396 (tm-30) REVERT: C 134 GLU cc_start: 0.7417 (tp30) cc_final: 0.6700 (tp30) REVERT: C 142 TYR cc_start: 0.8616 (t80) cc_final: 0.8050 (t80) REVERT: C 146 ASN cc_start: 0.8591 (m-40) cc_final: 0.8189 (m110) REVERT: D 83 TYR cc_start: 0.8673 (t80) cc_final: 0.8334 (t80) REVERT: D 96 TYR cc_start: 0.7658 (t80) cc_final: 0.6577 (t80) REVERT: D 128 LEU cc_start: 0.8768 (tp) cc_final: 0.8502 (tp) REVERT: E 100 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9123 (mt) REVERT: E 111 SER cc_start: 0.8301 (t) cc_final: 0.7974 (t) REVERT: E 134 GLU cc_start: 0.7527 (pp20) cc_final: 0.7225 (pp20) REVERT: E 138 LYS cc_start: 0.8720 (ptmm) cc_final: 0.8491 (ttpp) REVERT: F 64 ARG cc_start: 0.7755 (ttt-90) cc_final: 0.7554 (ttt-90) REVERT: F 154 MET cc_start: 0.7910 (tmm) cc_final: 0.7096 (ttt) REVERT: F 195 MET cc_start: 0.7517 (mmm) cc_final: 0.7230 (mmm) REVERT: G 134 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: H 378 THR cc_start: 0.9523 (t) cc_final: 0.9263 (m) REVERT: H 430 GLU cc_start: 0.7500 (tp30) cc_final: 0.6511 (tp30) REVERT: H 446 THR cc_start: 0.9307 (p) cc_final: 0.9097 (t) REVERT: H 447 TYR cc_start: 0.8526 (m-80) cc_final: 0.7703 (m-80) REVERT: I 74 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8528 (pp) REVERT: I 88 SER cc_start: 0.8997 (t) cc_final: 0.8386 (m) REVERT: I 114 LYS cc_start: 0.8756 (ptmt) cc_final: 0.8415 (ptmm) REVERT: J 429 GLN cc_start: 0.8114 (mm110) cc_final: 0.7881 (mm-40) REVERT: J 438 VAL cc_start: 0.9222 (m) cc_final: 0.8981 (p) REVERT: K 49 PHE cc_start: 0.8428 (m-10) cc_final: 0.8176 (m-10) REVERT: K 215 MET cc_start: 0.5436 (ppp) cc_final: 0.5166 (mmm) REVERT: L 79 ILE cc_start: 0.8962 (pt) cc_final: 0.8680 (mt) REVERT: L 169 GLU cc_start: 0.7740 (pp20) cc_final: 0.7520 (pp20) REVERT: M 420 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: N 19 ASP cc_start: 0.8065 (p0) cc_final: 0.7692 (p0) REVERT: N 192 LEU cc_start: 0.9150 (mm) cc_final: 0.8941 (mm) REVERT: O 34 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6900 (mp0) REVERT: O 136 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8532 (mm) REVERT: P 72 MET cc_start: 0.4995 (tmm) cc_final: 0.4498 (tmm) REVERT: Q 163 TYR cc_start: 0.2396 (t80) cc_final: 0.1645 (t80) REVERT: R 12 LYS cc_start: 0.6291 (tptt) cc_final: 0.6043 (tptp) REVERT: R 39 VAL cc_start: -0.1313 (OUTLIER) cc_final: -0.1740 (m) REVERT: R 83 LEU cc_start: 0.8427 (mt) cc_final: 0.7945 (tt) REVERT: R 165 MET cc_start: 0.7104 (mmm) cc_final: 0.6673 (tpp) REVERT: R 180 ASN cc_start: 0.7416 (p0) cc_final: 0.6145 (t0) REVERT: R 192 GLN cc_start: 0.7426 (tt0) cc_final: 0.7021 (tt0) REVERT: S 19 LEU cc_start: 0.5699 (tp) cc_final: 0.5449 (tp) REVERT: S 159 THR cc_start: 0.5106 (m) cc_final: 0.4676 (p) REVERT: S 180 ASN cc_start: 0.5998 (p0) cc_final: 0.5476 (p0) outliers start: 113 outliers final: 75 residues processed: 734 average time/residue: 0.1625 time to fit residues: 191.9736 Evaluate side-chains 707 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 625 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain J residue 423 ASP Chi-restraints excluded: chain J residue 468 THR Chi-restraints excluded: chain K residue 11 TRP Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 364 THR Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain M residue 433 LYS Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain P residue 48 ASN Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 182 VAL Chi-restraints excluded: chain Q residue 187 TYR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 175 optimal weight: 0.7980 chunk 284 optimal weight: 0.3980 chunk 259 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 285 optimal weight: 6.9990 chunk 314 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 317 optimal weight: 2.9990 chunk 280 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN D 156 HIS E 44 GLN ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN ** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 GLN ** N 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.103676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.094066 restraints weight = 100944.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.095844 restraints weight = 53305.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.097008 restraints weight = 32120.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.097813 restraints weight = 21498.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.098366 restraints weight = 15529.589| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.6460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28149 Z= 0.122 Angle : 0.665 13.803 38043 Z= 0.328 Chirality : 0.045 0.159 4287 Planarity : 0.004 0.046 4940 Dihedral : 4.636 35.279 3885 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.64 % Allowed : 25.20 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3543 helix: 0.02 (0.14), residues: 1423 sheet: -0.48 (0.23), residues: 524 loop : -1.40 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.029 0.001 TYR C 171 PHE 0.037 0.001 PHE N 92 TRP 0.013 0.001 TRP H 425 HIS 0.005 0.001 HIS H 366 Details of bonding type rmsd covalent geometry : bond 0.00290 (28149) covalent geometry : angle 0.66462 (38043) hydrogen bonds : bond 0.03073 ( 900) hydrogen bonds : angle 4.30971 ( 2661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 668 time to evaluate : 1.099 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: C 23 ARG cc_start: 0.8243 (mtm110) cc_final: 0.7983 (mtm110) REVERT: C 32 GLU cc_start: 0.6624 (tm-30) cc_final: 0.6399 (tm-30) REVERT: C 34 GLU cc_start: 0.6954 (mp0) cc_final: 0.6213 (mp0) REVERT: C 49 ASP cc_start: 0.6742 (t70) cc_final: 0.6537 (t70) REVERT: C 118 MET cc_start: 0.7871 (tmm) cc_final: 0.7624 (ttp) REVERT: C 142 TYR cc_start: 0.8602 (t80) cc_final: 0.8132 (t80) REVERT: C 146 ASN cc_start: 0.8567 (m-40) cc_final: 0.8151 (m110) REVERT: D 83 TYR cc_start: 0.8579 (t80) cc_final: 0.8301 (t80) REVERT: D 96 TYR cc_start: 0.7647 (t80) cc_final: 0.6582 (t80) REVERT: D 128 LEU cc_start: 0.8778 (tp) cc_final: 0.8520 (tp) REVERT: D 216 TYR cc_start: 0.8026 (t80) cc_final: 0.7790 (t80) REVERT: E 88 TYR cc_start: 0.8764 (m-80) cc_final: 0.8442 (m-80) REVERT: E 90 PHE cc_start: 0.8613 (m-10) cc_final: 0.7806 (m-80) REVERT: E 100 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9137 (mt) REVERT: E 111 SER cc_start: 0.8075 (t) cc_final: 0.7670 (t) REVERT: E 138 LYS cc_start: 0.8655 (ptmm) cc_final: 0.8447 (ttpp) REVERT: F 195 MET cc_start: 0.7558 (mmm) cc_final: 0.7277 (mmm) REVERT: G 134 GLU cc_start: 0.8206 (mp0) cc_final: 0.7828 (mp0) REVERT: G 139 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8005 (tm-30) REVERT: H 378 THR cc_start: 0.9495 (t) cc_final: 0.9268 (m) REVERT: H 430 GLU cc_start: 0.7374 (tp30) cc_final: 0.6392 (tp30) REVERT: H 447 TYR cc_start: 0.8492 (m-80) cc_final: 0.7740 (m-80) REVERT: I 74 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8501 (pp) REVERT: I 88 SER cc_start: 0.8949 (t) cc_final: 0.8415 (m) REVERT: I 114 LYS cc_start: 0.8686 (ptmt) cc_final: 0.8370 (ptmm) REVERT: J 429 GLN cc_start: 0.8136 (mm110) cc_final: 0.7834 (mm-40) REVERT: J 438 VAL cc_start: 0.9206 (m) cc_final: 0.8987 (p) REVERT: K 49 PHE cc_start: 0.8423 (m-10) cc_final: 0.8178 (m-10) REVERT: K 215 MET cc_start: 0.5538 (ppp) cc_final: 0.5306 (mmm) REVERT: L 79 ILE cc_start: 0.8954 (pt) cc_final: 0.8684 (mt) REVERT: M 399 GLU cc_start: 0.7788 (mp0) cc_final: 0.7254 (mp0) REVERT: M 420 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: N 19 ASP cc_start: 0.7992 (p0) cc_final: 0.7765 (p0) REVERT: N 25 PHE cc_start: 0.8769 (t80) cc_final: 0.8507 (t80) REVERT: N 47 GLU cc_start: 0.8104 (tp30) cc_final: 0.7447 (tp30) REVERT: N 190 ASP cc_start: 0.5711 (t70) cc_final: 0.5377 (t0) REVERT: N 199 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7492 (pm20) REVERT: N 244 ASP cc_start: 0.7329 (p0) cc_final: 0.6754 (p0) REVERT: O 37 GLU cc_start: 0.7119 (pt0) cc_final: 0.6852 (pt0) REVERT: O 45 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7955 (tpp) REVERT: O 93 ILE cc_start: 0.8772 (mp) cc_final: 0.8366 (mt) REVERT: O 97 ASP cc_start: 0.7077 (t70) cc_final: 0.6835 (t0) REVERT: O 136 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8271 (mm) REVERT: P 72 MET cc_start: 0.4952 (tmm) cc_final: 0.4450 (tmm) REVERT: P 101 LYS cc_start: 0.6412 (mmtm) cc_final: 0.6197 (mmtp) REVERT: Q 163 TYR cc_start: 0.2413 (t80) cc_final: 0.1544 (t80) REVERT: Q 192 MET cc_start: 0.4478 (mpp) cc_final: 0.4040 (mpp) REVERT: R 39 VAL cc_start: -0.1738 (OUTLIER) cc_final: -0.2131 (m) REVERT: R 83 LEU cc_start: 0.8477 (mt) cc_final: 0.7942 (tt) REVERT: R 165 MET cc_start: 0.7190 (mmm) cc_final: 0.6910 (tpp) REVERT: R 180 ASN cc_start: 0.7059 (p0) cc_final: 0.6173 (t0) REVERT: R 192 GLN cc_start: 0.7478 (tt0) cc_final: 0.7041 (tt0) REVERT: S 19 LEU cc_start: 0.5674 (tp) cc_final: 0.5397 (tp) REVERT: S 159 THR cc_start: 0.4996 (m) cc_final: 0.4577 (p) REVERT: S 180 ASN cc_start: 0.6292 (p0) cc_final: 0.5758 (p0) outliers start: 78 outliers final: 58 residues processed: 717 average time/residue: 0.1615 time to fit residues: 186.0672 Evaluate side-chains 690 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 625 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 182 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 296 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 260 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 333 optimal weight: 0.9990 chunk 245 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN B 75 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN ** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.101718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.092364 restraints weight = 101001.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.094140 restraints weight = 53217.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.095264 restraints weight = 32076.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.096062 restraints weight = 21501.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.096599 restraints weight = 15478.704| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28149 Z= 0.160 Angle : 0.707 13.970 38043 Z= 0.351 Chirality : 0.046 0.157 4287 Planarity : 0.004 0.049 4940 Dihedral : 4.788 41.420 3885 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.31 % Allowed : 25.03 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 3543 helix: -0.05 (0.14), residues: 1447 sheet: -0.45 (0.24), residues: 508 loop : -1.50 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 164 TYR 0.031 0.001 TYR N 185 PHE 0.033 0.002 PHE I 102 TRP 0.017 0.001 TRP H 425 HIS 0.006 0.001 HIS H 366 Details of bonding type rmsd covalent geometry : bond 0.00376 (28149) covalent geometry : angle 0.70668 (38043) hydrogen bonds : bond 0.03192 ( 900) hydrogen bonds : angle 4.41546 ( 2661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 653 time to evaluate : 0.942 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: A 138 MET cc_start: 0.7145 (mmm) cc_final: 0.6448 (mmp) REVERT: B 49 ARG cc_start: 0.8793 (ttp-110) cc_final: 0.8105 (mtp-110) REVERT: C 23 ARG cc_start: 0.8229 (mtm110) cc_final: 0.7949 (mtm110) REVERT: C 32 GLU cc_start: 0.6598 (tm-30) cc_final: 0.6368 (tm-30) REVERT: C 34 GLU cc_start: 0.6933 (mp0) cc_final: 0.6190 (mp0) REVERT: C 142 TYR cc_start: 0.8715 (t80) cc_final: 0.8192 (t80) REVERT: C 146 ASN cc_start: 0.8571 (m-40) cc_final: 0.8198 (m110) REVERT: D 83 TYR cc_start: 0.8651 (t80) cc_final: 0.8355 (t80) REVERT: D 96 TYR cc_start: 0.7568 (t80) cc_final: 0.6546 (t80) REVERT: D 128 LEU cc_start: 0.8775 (tp) cc_final: 0.8535 (tp) REVERT: E 100 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9128 (mt) REVERT: E 111 SER cc_start: 0.8444 (t) cc_final: 0.8137 (t) REVERT: E 134 GLU cc_start: 0.7567 (pp20) cc_final: 0.7206 (pp20) REVERT: E 135 ILE cc_start: 0.8985 (tp) cc_final: 0.8729 (pt) REVERT: F 195 MET cc_start: 0.7485 (mmm) cc_final: 0.7116 (mmm) REVERT: G 134 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: G 139 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7988 (tm-30) REVERT: H 378 THR cc_start: 0.9513 (t) cc_final: 0.9281 (m) REVERT: H 430 GLU cc_start: 0.7467 (tp30) cc_final: 0.6522 (tp30) REVERT: H 447 TYR cc_start: 0.8496 (m-80) cc_final: 0.7693 (m-80) REVERT: I 74 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8519 (pp) REVERT: I 88 SER cc_start: 0.9025 (t) cc_final: 0.8389 (m) REVERT: J 429 GLN cc_start: 0.8157 (mm110) cc_final: 0.7917 (mm-40) REVERT: J 438 VAL cc_start: 0.9169 (m) cc_final: 0.8951 (p) REVERT: K 49 PHE cc_start: 0.8403 (m-10) cc_final: 0.8173 (m-10) REVERT: K 215 MET cc_start: 0.5435 (ppp) cc_final: 0.5032 (mmm) REVERT: L 79 ILE cc_start: 0.8957 (pt) cc_final: 0.8734 (mt) REVERT: L 169 GLU cc_start: 0.7696 (pp20) cc_final: 0.7342 (tm-30) REVERT: M 420 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: N 19 ASP cc_start: 0.7999 (p0) cc_final: 0.7659 (p0) REVERT: N 25 PHE cc_start: 0.8854 (t80) cc_final: 0.8551 (t80) REVERT: N 47 GLU cc_start: 0.8167 (tp30) cc_final: 0.7701 (tp30) REVERT: N 98 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8165 (p) REVERT: N 160 GLU cc_start: 0.7158 (tp30) cc_final: 0.6479 (tp30) REVERT: N 199 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: N 244 ASP cc_start: 0.7338 (p0) cc_final: 0.6108 (p0) REVERT: N 248 LYS cc_start: 0.8429 (mttp) cc_final: 0.7507 (mttp) REVERT: O 37 GLU cc_start: 0.7127 (pt0) cc_final: 0.6837 (pt0) REVERT: O 136 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8400 (mm) REVERT: P 16 MET cc_start: 0.7058 (tpt) cc_final: 0.6853 (tpt) REVERT: P 72 MET cc_start: 0.5087 (tmm) cc_final: 0.4547 (tmm) REVERT: Q 163 TYR cc_start: 0.2351 (t80) cc_final: 0.1590 (t80) REVERT: Q 192 MET cc_start: 0.4532 (mpp) cc_final: 0.4017 (mpp) REVERT: R 12 LYS cc_start: 0.5590 (tptp) cc_final: 0.4903 (tptt) REVERT: R 39 VAL cc_start: -0.0783 (OUTLIER) cc_final: -0.1076 (m) REVERT: R 165 MET cc_start: 0.7030 (mmm) cc_final: 0.6661 (tpp) REVERT: R 180 ASN cc_start: 0.7004 (p0) cc_final: 0.6147 (t0) REVERT: S 19 LEU cc_start: 0.5646 (tp) cc_final: 0.5327 (tp) REVERT: S 159 THR cc_start: 0.5150 (m) cc_final: 0.4707 (p) REVERT: S 180 ASN cc_start: 0.5966 (p0) cc_final: 0.5382 (p0) outliers start: 98 outliers final: 70 residues processed: 713 average time/residue: 0.1585 time to fit residues: 181.3378 Evaluate side-chains 708 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 630 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 165 TYR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 423 ASP Chi-restraints excluded: chain K residue 11 TRP Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 47 GLN Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 364 THR Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 402 VAL Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 182 VAL Chi-restraints excluded: chain Q residue 187 TYR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 220 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 253 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN ** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 GLN N 143 GLN N 204 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.101060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.091763 restraints weight = 101134.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.093534 restraints weight = 53188.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.094660 restraints weight = 31989.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.095448 restraints weight = 21351.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.096015 restraints weight = 15462.923| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28149 Z= 0.167 Angle : 0.727 14.011 38043 Z= 0.362 Chirality : 0.046 0.163 4287 Planarity : 0.004 0.050 4940 Dihedral : 4.938 46.841 3885 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.97 % Allowed : 25.37 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.17 (0.14), residues: 3543 helix: -0.06 (0.14), residues: 1457 sheet: -0.50 (0.24), residues: 487 loop : -1.49 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 17 TYR 0.043 0.002 TYR C 171 PHE 0.043 0.002 PHE N 92 TRP 0.018 0.002 TRP H 425 HIS 0.006 0.002 HIS H 366 Details of bonding type rmsd covalent geometry : bond 0.00396 (28149) covalent geometry : angle 0.72731 (38043) hydrogen bonds : bond 0.03184 ( 900) hydrogen bonds : angle 4.46108 ( 2661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 649 time to evaluate : 0.992 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: B 49 ARG cc_start: 0.8709 (ttp-110) cc_final: 0.8156 (mtp-110) REVERT: C 23 ARG cc_start: 0.8183 (mtm110) cc_final: 0.7879 (mtm110) REVERT: C 32 GLU cc_start: 0.6607 (tm-30) cc_final: 0.6384 (tm-30) REVERT: C 34 GLU cc_start: 0.7023 (mp0) cc_final: 0.6316 (mp0) REVERT: C 78 MET cc_start: 0.8250 (mtp) cc_final: 0.7932 (ptp) REVERT: C 142 TYR cc_start: 0.8709 (t80) cc_final: 0.8208 (t80) REVERT: C 146 ASN cc_start: 0.8616 (m-40) cc_final: 0.8224 (m-40) REVERT: C 167 ASP cc_start: 0.8401 (p0) cc_final: 0.8096 (p0) REVERT: D 83 TYR cc_start: 0.8706 (t80) cc_final: 0.8449 (t80) REVERT: D 96 TYR cc_start: 0.7560 (t80) cc_final: 0.6537 (t80) REVERT: E 100 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9199 (mt) REVERT: E 111 SER cc_start: 0.8499 (t) cc_final: 0.8215 (t) REVERT: E 136 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8467 (mm-40) REVERT: F 163 GLN cc_start: 0.6362 (mm110) cc_final: 0.5788 (pm20) REVERT: F 195 MET cc_start: 0.7361 (mmm) cc_final: 0.7069 (mmm) REVERT: G 39 ASP cc_start: 0.7714 (p0) cc_final: 0.7306 (p0) REVERT: G 139 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8034 (tm-30) REVERT: H 378 THR cc_start: 0.9524 (t) cc_final: 0.9274 (m) REVERT: H 430 GLU cc_start: 0.7488 (tp30) cc_final: 0.6774 (tp30) REVERT: H 447 TYR cc_start: 0.8435 (m-80) cc_final: 0.7681 (m-80) REVERT: I 74 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8501 (pp) REVERT: I 88 SER cc_start: 0.8958 (t) cc_final: 0.8335 (m) REVERT: J 429 GLN cc_start: 0.8174 (mm110) cc_final: 0.7922 (mm-40) REVERT: K 49 PHE cc_start: 0.8343 (m-10) cc_final: 0.8120 (m-10) REVERT: K 215 MET cc_start: 0.6011 (ppp) cc_final: 0.5348 (mmm) REVERT: L 79 ILE cc_start: 0.8944 (pt) cc_final: 0.8694 (mt) REVERT: L 169 GLU cc_start: 0.7821 (pp20) cc_final: 0.7553 (tm-30) REVERT: M 420 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: N 19 ASP cc_start: 0.8001 (p0) cc_final: 0.7661 (p0) REVERT: N 25 PHE cc_start: 0.8904 (t80) cc_final: 0.8541 (t80) REVERT: N 47 GLU cc_start: 0.8162 (tp30) cc_final: 0.7684 (tp30) REVERT: N 98 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8191 (p) REVERT: N 146 GLU cc_start: 0.7019 (pp20) cc_final: 0.6806 (pp20) REVERT: N 199 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: N 244 ASP cc_start: 0.7199 (p0) cc_final: 0.5961 (p0) REVERT: N 248 LYS cc_start: 0.8472 (mttp) cc_final: 0.7553 (mttp) REVERT: O 93 ILE cc_start: 0.8724 (mp) cc_final: 0.8349 (mt) REVERT: O 136 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8421 (mm) REVERT: P 16 MET cc_start: 0.7059 (tpt) cc_final: 0.6856 (tpt) REVERT: P 28 ILE cc_start: 0.6385 (OUTLIER) cc_final: 0.6139 (mt) REVERT: P 72 MET cc_start: 0.5098 (tmm) cc_final: 0.4685 (tmm) REVERT: Q 163 TYR cc_start: 0.2374 (t80) cc_final: 0.1633 (t80) REVERT: Q 192 MET cc_start: 0.4515 (mpp) cc_final: 0.4005 (mpp) REVERT: R 39 VAL cc_start: -0.0847 (OUTLIER) cc_final: -0.1105 (m) REVERT: R 165 MET cc_start: 0.7059 (mmm) cc_final: 0.6722 (tpp) REVERT: S 19 LEU cc_start: 0.5780 (tp) cc_final: 0.5504 (tp) REVERT: S 157 ASN cc_start: 0.7280 (p0) cc_final: 0.6333 (p0) REVERT: S 163 THR cc_start: 0.4210 (p) cc_final: 0.3876 (t) REVERT: S 180 ASN cc_start: 0.6013 (OUTLIER) cc_final: 0.5382 (p0) outliers start: 88 outliers final: 70 residues processed: 703 average time/residue: 0.1648 time to fit residues: 184.3417 Evaluate side-chains 706 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 627 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 165 TYR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 423 ASP Chi-restraints excluded: chain K residue 11 TRP Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 47 GLN Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain M residue 364 THR Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 402 VAL Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain M residue 433 LYS Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 182 VAL Chi-restraints excluded: chain Q residue 187 TYR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 180 ASN Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 315 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 272 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 127 optimal weight: 0.0570 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 226 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 GLN J 407 HIS ** J 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.103309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.094004 restraints weight = 100229.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.095817 restraints weight = 52358.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.096913 restraints weight = 31083.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.097741 restraints weight = 20639.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.098217 restraints weight = 14825.064| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.6980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28149 Z= 0.124 Angle : 0.711 13.628 38043 Z= 0.348 Chirality : 0.045 0.289 4287 Planarity : 0.004 0.070 4940 Dihedral : 4.753 43.630 3885 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.30 % Allowed : 26.45 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.04 (0.14), residues: 3543 helix: 0.09 (0.14), residues: 1426 sheet: -0.43 (0.24), residues: 510 loop : -1.45 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.028 0.001 TYR N 185 PHE 0.033 0.001 PHE I 102 TRP 0.021 0.001 TRP L 208 HIS 0.006 0.001 HIS H 366 Details of bonding type rmsd covalent geometry : bond 0.00294 (28149) covalent geometry : angle 0.71068 (38043) hydrogen bonds : bond 0.03069 ( 900) hydrogen bonds : angle 4.35343 ( 2661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4899.63 seconds wall clock time: 85 minutes 11.79 seconds (5111.79 seconds total)