Starting phenix.real_space_refine on Sun Sep 13 04:42:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21gf_67646/09_2026/21gf_67646.cif Found real_map, /net/cci-nas-00/data/ceres_data/21gf_67646/09_2026/21gf_67646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21gf_67646/09_2026/21gf_67646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21gf_67646/09_2026/21gf_67646.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21gf_67646/09_2026/21gf_67646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21gf_67646/09_2026/21gf_67646.map" } resolution = 3.75 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= 0.001 sd= 0.062 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: 5 Type Number sf(0) Gaussians S 49 5.16 5 C 10304 2.51 5 N 2807 2.21 5 O 3255 1.98 5 H 4007 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20422 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2925 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2909 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2909 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "D" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2928 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "E" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2911 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "F" Number of atoms: 2920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2920 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "G" Number of atoms: 2920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2920 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Time building chain proxies: 4.34, per 1000 atoms: 0.21 Number of scatterers: 20422 At special positions: 0 Unit cell: (111.32, 115, 115, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 O 3255 8.00 N 2807 7.00 C 10304 6.00 H 4007 1.00 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: 1.66 Conformation dependent library (CDL) restraints added in 732.7 milliseconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3794 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 28 sheets defined 6.3% alpha, 55.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'B' and resid 1 through 6 removed outlier: 3.527A pdb=" N ASN B 6 " --> pdb=" O SER B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 217 through 222 removed outlier: 4.386A pdb=" N SER B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 217 through 222 removed outlier: 4.399A pdb=" N SER C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 6 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 212 through 216 Processing helix chain 'E' and resid 1 through 6 Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 212 through 216 Processing helix chain 'F' and resid 1 through 6 removed outlier: 3.511A pdb=" N ASN F 6 " --> pdb=" O SER F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 212 through 216 Processing helix chain 'G' and resid 1 through 6 removed outlier: 3.527A pdb=" N ASN G 6 " --> pdb=" O SER G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 209 Processing helix chain 'G' and resid 212 through 216 Processing helix chain 'G' and resid 217 through 222 removed outlier: 4.351A pdb=" N SER G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 29 removed outlier: 3.876A pdb=" N ASP A 100 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR A 233 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE A 98 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 78 removed outlier: 6.338A pdb=" N ASP A 254 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N SER A 82 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 78 removed outlier: 7.400A pdb=" N ASP A 255 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASP A 272 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N GLN A 257 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR A 270 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N HIS A 259 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N THR A 268 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 127 removed outlier: 3.558A pdb=" N GLY G 126 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS G 110 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR G 109 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N VAL G 149 " --> pdb=" O THR G 109 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR G 145 " --> pdb=" O MET G 113 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR G 115 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY E 126 " --> pdb=" O GLY F 134 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU F 146 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR E 115 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY E 143 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR E 125 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL D 124 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR D 125 " --> pdb=" O GLY D 133 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY C 126 " --> pdb=" O GLY D 134 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 110 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR C 109 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL C 149 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR C 125 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 133 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 126 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS B 110 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR B 109 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL B 149 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 115 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B 125 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 126 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 118 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 176 removed outlier: 6.262A pdb=" N MET A 174 " --> pdb=" O PRO A 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 29 removed outlier: 3.582A pdb=" N ILE B 43 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP B 100 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR B 233 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE B 98 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 70 removed outlier: 6.494A pdb=" N GLY B 77 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLU B 70 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LYS B 75 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N SER B 82 " --> pdb=" O PHE B 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 70 removed outlier: 6.494A pdb=" N GLY B 77 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLU B 70 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LYS B 75 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP B 80 " --> pdb=" O ASP B 254 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 252 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 84 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU B 250 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 86 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 248 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 88 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASP B 246 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP B 255 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ASP B 272 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLN B 257 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N THR B 270 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N HIS B 259 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR B 268 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 176 removed outlier: 7.247A pdb=" N ASN B 176 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLY B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 20 through 29 removed outlier: 3.560A pdb=" N MET C 34 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 228 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C 229 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR C 101 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 231 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.605A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU C 70 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS C 75 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N SER C 82 " --> pdb=" O PHE C 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.605A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU C 70 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS C 75 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP C 80 " --> pdb=" O ASP C 254 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C 252 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE C 84 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU C 250 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL C 86 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE C 248 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU C 88 " --> pdb=" O ASP C 246 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP C 246 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ASP C 255 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP C 272 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLN C 257 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR C 270 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N HIS C 259 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR C 268 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 290 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 29 removed outlier: 3.571A pdb=" N MET D 34 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR D 233 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE D 98 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 153 through 157 removed outlier: 8.173A pdb=" N SER D 82 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LYS D 75 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TRP D 260 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLY D 77 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU D 258 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ALA D 79 " --> pdb=" O TYR D 256 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR D 256 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP D 254 " --> pdb=" O PRO D 81 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 83 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP D 255 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP D 272 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N GLN D 257 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N THR D 270 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N HIS D 259 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR D 268 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 290 " --> pdb=" O ASP D 285 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 174 through 176 removed outlier: 7.242A pdb=" N ASN D 176 " --> pdb=" O GLY D 180 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLY D 180 " --> pdb=" O ASN D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 21 through 29 removed outlier: 3.551A pdb=" N MET E 34 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE E 43 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP E 100 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR E 233 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE E 98 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 66 through 70 removed outlier: 6.448A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU E 70 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS E 75 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N SER E 82 " --> pdb=" O PHE E 171 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 66 through 70 removed outlier: 6.448A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU E 70 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS E 75 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP E 80 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL E 252 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE E 84 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLU E 250 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL E 86 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE E 248 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU E 88 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP E 246 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASP E 255 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASP E 272 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N GLN E 257 " --> pdb=" O THR E 270 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N THR E 270 " --> pdb=" O GLN E 257 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N HIS E 259 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR E 268 " --> pdb=" O HIS E 259 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 174 through 176 removed outlier: 7.233A pdb=" N ASN E 176 " --> pdb=" O GLY E 180 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLY E 180 " --> pdb=" O ASN E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 20 through 29 removed outlier: 3.551A pdb=" N MET F 34 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE F 43 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE F 228 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP F 100 " --> pdb=" O VAL F 231 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR F 233 " --> pdb=" O ILE F 98 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE F 98 " --> pdb=" O THR F 233 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 66 through 70 removed outlier: 5.769A pdb=" N VAL F 67 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA F 79 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER F 69 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N SER F 82 " --> pdb=" O PHE F 171 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 66 through 70 removed outlier: 5.769A pdb=" N VAL F 67 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA F 79 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER F 69 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP F 80 " --> pdb=" O ASP F 254 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL F 252 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE F 84 " --> pdb=" O GLU F 250 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLU F 250 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL F 86 " --> pdb=" O ILE F 248 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE F 248 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU F 88 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP F 246 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ASP F 255 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP F 272 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N GLN F 257 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR F 270 " --> pdb=" O GLN F 257 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS F 259 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N THR F 268 " --> pdb=" O HIS F 259 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 174 through 176 removed outlier: 7.194A pdb=" N ASN F 176 " --> pdb=" O GLY F 180 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY F 180 " --> pdb=" O ASN F 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 20 through 23 removed outlier: 3.628A pdb=" N MET G 34 " --> pdb=" O ASP G 29 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 20 through 23 removed outlier: 6.844A pdb=" N ALA G 229 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR G 101 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL G 231 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 66 through 70 removed outlier: 6.474A pdb=" N GLY G 77 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU G 70 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS G 75 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N SER G 82 " --> pdb=" O PHE G 171 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 66 through 70 removed outlier: 6.474A pdb=" N GLY G 77 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU G 70 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS G 75 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP G 80 " --> pdb=" O ASP G 254 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL G 252 " --> pdb=" O SER G 82 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE G 84 " --> pdb=" O GLU G 250 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU G 250 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL G 86 " --> pdb=" O ILE G 248 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE G 248 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU G 88 " --> pdb=" O ASP G 246 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASP G 246 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASP G 255 " --> pdb=" O ASP G 272 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP G 272 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLN G 257 " --> pdb=" O THR G 270 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR G 270 " --> pdb=" O GLN G 257 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N HIS G 259 " --> pdb=" O THR G 268 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR G 268 " --> pdb=" O HIS G 259 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 174 through 176 removed outlier: 7.226A pdb=" N ASN G 176 " --> pdb=" O GLY G 180 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY G 180 " --> pdb=" O ASN G 176 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 1899 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4007 1.03 - 1.22: 11 1.22 - 1.42: 7199 1.42 - 1.61: 9471 1.61 - 1.80: 98 Bond restraints: 20786 Sorted by residual: bond pdb=" C LYS E 58 " pdb=" N GLY E 59 " ideal model delta sigma weight residual 1.335 1.321 0.013 7.50e-03 1.78e+04 3.21e+00 bond pdb=" C LYS B 58 " pdb=" N GLY B 59 " ideal model delta sigma weight residual 1.335 1.323 0.012 7.50e-03 1.78e+04 2.56e+00 bond pdb=" C GLN F 150 " pdb=" O GLN F 150 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 2.08e+00 bond pdb=" C GLN F 89 " pdb=" N LEU F 90 " ideal model delta sigma weight residual 1.329 1.309 0.019 1.60e-02 3.91e+03 1.46e+00 bond pdb=" CA LEU C 53 " pdb=" C LEU C 53 " ideal model delta sigma weight residual 1.529 1.517 0.012 1.04e-02 9.25e+03 1.34e+00 ... (remaining 20781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 28159 0.90 - 1.80: 1520 1.80 - 2.70: 194 2.70 - 3.60: 59 3.60 - 4.50: 7 Bond angle restraints: 29939 Sorted by residual: angle pdb=" N ILE C 5 " pdb=" CA ILE C 5 " pdb=" C ILE C 5 " ideal model delta sigma weight residual 112.29 109.01 3.28 9.40e-01 1.13e+00 1.22e+01 angle pdb=" N SER A 262 " pdb=" CA SER A 262 " pdb=" CB SER A 262 " ideal model delta sigma weight residual 114.17 110.25 3.92 1.14e+00 7.69e-01 1.18e+01 angle pdb=" N ILE F 5 " pdb=" CA ILE F 5 " pdb=" C ILE F 5 " ideal model delta sigma weight residual 112.17 109.05 3.12 9.50e-01 1.11e+00 1.08e+01 angle pdb=" N ILE G 5 " pdb=" CA ILE G 5 " pdb=" C ILE G 5 " ideal model delta sigma weight residual 112.17 109.05 3.12 9.50e-01 1.11e+00 1.08e+01 angle pdb=" N ILE E 5 " pdb=" CA ILE E 5 " pdb=" C ILE E 5 " ideal model delta sigma weight residual 111.91 109.00 2.91 8.90e-01 1.26e+00 1.07e+01 ... (remaining 29934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 11991 17.73 - 35.46: 763 35.46 - 53.19: 193 53.19 - 70.92: 34 70.92 - 88.65: 11 Dihedral angle restraints: 12992 sinusoidal: 6958 harmonic: 6034 Sorted by residual: dihedral pdb=" CA GLN C 257 " pdb=" CB GLN C 257 " pdb=" CG GLN C 257 " pdb=" CD GLN C 257 " ideal model delta sinusoidal sigma weight residual -180.00 -120.32 -59.68 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB LYS F 30 " pdb=" CG LYS F 30 " pdb=" CD LYS F 30 " pdb=" CE LYS F 30 " ideal model delta sinusoidal sigma weight residual -180.00 -121.81 -58.19 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA ASP E 254 " pdb=" CB ASP E 254 " pdb=" CG ASP E 254 " pdb=" OD1 ASP E 254 " ideal model delta sinusoidal sigma weight residual -30.00 -82.71 52.71 1 2.00e+01 2.50e-03 9.46e+00 ... (remaining 12989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1327 0.027 - 0.055: 675 0.055 - 0.082: 186 0.082 - 0.110: 168 0.110 - 0.137: 73 Chirality restraints: 2429 Sorted by residual: chirality pdb=" CA VAL C 86 " pdb=" N VAL C 86 " pdb=" C VAL C 86 " pdb=" CB VAL C 86 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA VAL G 86 " pdb=" N VAL G 86 " pdb=" C VAL G 86 " pdb=" CB VAL G 86 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA VAL A 86 " pdb=" N VAL A 86 " pdb=" C VAL A 86 " pdb=" CB VAL A 86 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 2426 not shown) Planarity restraints: 4914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.010 2.00e-02 2.50e+03 1.53e-02 3.52e+00 pdb=" CG ASN A 176 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 176 " 0.003 2.00e-02 2.50e+03 pdb="HD22 ASN A 176 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 93 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.77e+00 pdb=" C ASN D 93 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN D 93 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU D 94 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 208 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.06e+00 pdb=" C ASP D 208 " -0.025 2.00e-02 2.50e+03 pdb=" O ASP D 208 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN D 209 " 0.008 2.00e-02 2.50e+03 ... (remaining 4911 not shown) Histogram of nonbonded interaction distances: 1.29 - 1.95: 24 1.95 - 2.61: 7825 2.61 - 3.28: 30500 3.28 - 3.94: 48320 3.94 - 4.60: 70269 Nonbonded interactions: 156938 Sorted by model distance: nonbonded pdb=" O ASN B 201 " pdb="HD21 ASN B 201 " model vdw 1.289 2.450 nonbonded pdb=" H SER A 222 " pdb=" HG SER A 222 " model vdw 1.891 2.100 nonbonded pdb=" H SER C 222 " pdb=" HG SER C 222 " model vdw 1.893 2.100 nonbonded pdb="HD21 ASN A 49 " pdb=" HH TYR B 40 " model vdw 1.899 2.100 nonbonded pdb=" HG SER F 82 " pdb="HH12 ARG F 184 " model vdw 1.912 2.100 ... (remaining 156933 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HE or name HH11 or name HH12 or name HH21 or name HH \ 22)) or resid 67 through 74 or (resid 75 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ or name H or name HZ1 \ or name HZ2 or name HZ3)) or resid 76 through 293)) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HZ1 or name HZ2 or name HZ3)) or resid 31 through 239 or (resid 240 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE o \ r name NZ or name H or name HZ1 or name HZ2 or name HZ3)) or resid 241 through 2 \ 58 or (resid 259 and (name N or name CA or name C or name O or name CB or name C \ G or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HE2)) or res \ id 260 through 293)) selection = (chain 'E' and (resid 1 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HE2)) or resid 36 through 258 or (resid 259 and (name N or na \ me CA or name C or name O or name CB or name CG or name ND1 or name CD2 or name \ CE1 or name NE2 or name H or name HE2)) or resid 260 through 293)) selection = (chain 'F' and (resid 1 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HE2)) or resid 36 through 258 or (resid 259 and (name N or na \ me CA or name C or name O or name CB or name CG or name ND1 or name CD2 or name \ CE1 or name NE2 or name H or name HE2)) or resid 260 through 282 or (resid 283 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me CE or name NZ or name H or name HZ1 or name HZ2 or name HZ3)) or resid 284 th \ rough 293)) selection = (chain 'G' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HZ1 or name HZ2 or name HZ3)) or resid 31 through 34 or (resid 35 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 o \ r name CE1 or name NE2 or name H or name HE2)) or resid 36 through 258 or (resid \ 259 and (name N or name CA or name C or name O or name CB or name CG or name ND \ 1 or name CD2 or name CE1 or name NE2 or name H or name HE2)) or resid 260 throu \ gh 293)) } 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: 1.390 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: 0.180 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.660 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.004 0.031 16779 Z= 0.181 Angle : 0.504 4.499 22715 Z= 0.305 Chirality : 0.045 0.137 2429 Planarity : 0.003 0.026 2933 Dihedral : 13.692 88.647 6174 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.05 % Allowed : 12.63 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.18), residues: 2037 helix: None (None), residues: 0 sheet: -0.47 (0.15), residues: 1141 loop : -0.23 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 253 TYR 0.011 0.001 TYR E 65 PHE 0.009 0.001 PHE B 84 TRP 0.013 0.001 TRP A 179 HIS 0.003 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (16779) covalent geometry : angle 0.50446 / 0.30 (22715) hydrogen bonds : bond 0.26681 / 17.51 ( 699) hydrogen bonds : angle 11.21440 / 7.71 ( 1899) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 SER cc_start: 0.9153 (t) cc_final: 0.8845 (p) REVERT: A 208 ASP cc_start: 0.8178 (m-30) cc_final: 0.7873 (t0) REVERT: B 3 SER cc_start: 0.9385 (p) cc_final: 0.9132 (t) REVERT: B 135 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7487 (tt) REVERT: B 208 ASP cc_start: 0.8438 (m-30) cc_final: 0.8119 (t70) REVERT: B 285 ASP cc_start: 0.8203 (t0) cc_final: 0.7682 (t0) REVERT: C 3 SER cc_start: 0.9283 (p) cc_final: 0.9065 (t) REVERT: D 76 SER cc_start: 0.9299 (t) cc_final: 0.9017 (p) REVERT: D 152 ASP cc_start: 0.8306 (m-30) cc_final: 0.8066 (t0) REVERT: E 164 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.6984 (tttm) REVERT: E 208 ASP cc_start: 0.8042 (t70) cc_final: 0.7804 (t0) REVERT: F 208 ASP cc_start: 0.8195 (m-30) cc_final: 0.7845 (t70) REVERT: G 208 ASP cc_start: 0.8200 (m-30) cc_final: 0.7851 (t0) outliers start: 19 outliers final: 16 residues processed: 217 average time/residue: 0.1381 time to fit residues: 48.4443 Evaluate side-chains 213 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 117 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN B 123 ASN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.119950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.092570 restraints weight = 28991.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.095821 restraints weight = 18295.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.098116 restraints weight = 13387.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.099595 restraints weight = 10909.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.100450 restraints weight = 9466.347| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16779 Z= 0.165 Angle : 0.470 4.055 22715 Z= 0.263 Chirality : 0.046 0.154 2429 Planarity : 0.003 0.021 2933 Dihedral : 5.070 59.445 2253 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.99 % Allowed : 11.86 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.18), residues: 2037 helix: None (None), residues: 0 sheet: -0.11 (0.15), residues: 1141 loop : -0.25 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 56 TYR 0.014 0.002 TYR C 148 PHE 0.011 0.001 PHE B 84 TRP 0.008 0.001 TRP F 286 HIS 0.004 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (16779) covalent geometry : angle 0.47034 / 0.26 (22715) hydrogen bonds : bond 0.04163 / 2.75 ( 699) hydrogen bonds : angle 6.69787 / 4.67 ( 1899) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.8166 (m-30) cc_final: 0.7744 (t0) REVERT: B 3 SER cc_start: 0.9433 (p) cc_final: 0.9166 (t) REVERT: B 204 MET cc_start: 0.7763 (pmm) cc_final: 0.7329 (pmm) REVERT: B 208 ASP cc_start: 0.8556 (m-30) cc_final: 0.8236 (t70) REVERT: B 264 ASN cc_start: 0.8951 (p0) cc_final: 0.8737 (p0) REVERT: D 76 SER cc_start: 0.9306 (t) cc_final: 0.9013 (p) REVERT: D 152 ASP cc_start: 0.8379 (m-30) cc_final: 0.7931 (t0) REVERT: E 164 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7151 (tttm) REVERT: E 208 ASP cc_start: 0.8261 (t70) cc_final: 0.7966 (t0) REVERT: F 208 ASP cc_start: 0.8380 (m-30) cc_final: 0.7983 (t70) REVERT: G 208 ASP cc_start: 0.8351 (m-30) cc_final: 0.8004 (t0) outliers start: 36 outliers final: 24 residues processed: 211 average time/residue: 0.1413 time to fit residues: 47.5360 Evaluate side-chains 201 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 276 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 127 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.117123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.089846 restraints weight = 29447.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.092984 restraints weight = 18892.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.095096 restraints weight = 14115.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.096402 restraints weight = 11572.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.097413 restraints weight = 10157.435| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 16779 Z= 0.254 Angle : 0.530 4.435 22715 Z= 0.295 Chirality : 0.047 0.146 2429 Planarity : 0.003 0.029 2933 Dihedral : 4.828 46.821 2230 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.87 % Allowed : 12.41 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2037 helix: None (None), residues: 0 sheet: -0.07 (0.15), residues: 1127 loop : -0.55 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.017 0.002 TYR D 148 PHE 0.015 0.002 PHE D 84 TRP 0.009 0.001 TRP A 80 HIS 0.005 0.001 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.25 (16779) covalent geometry : angle 0.52963 / 0.29 (22715) hydrogen bonds : bond 0.03713 / 2.45 ( 699) hydrogen bonds : angle 6.04556 / 4.20 ( 1899) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.8110 (m-30) cc_final: 0.7824 (t0) REVERT: A 208 ASP cc_start: 0.8416 (t0) cc_final: 0.7932 (t0) REVERT: B 3 SER cc_start: 0.9438 (p) cc_final: 0.9189 (t) REVERT: B 204 MET cc_start: 0.7864 (pmm) cc_final: 0.7504 (pmm) REVERT: B 208 ASP cc_start: 0.8526 (m-30) cc_final: 0.8226 (t70) REVERT: B 264 ASN cc_start: 0.8938 (p0) cc_final: 0.8635 (p0) REVERT: C 5 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7593 (mt) REVERT: D 76 SER cc_start: 0.9284 (t) cc_final: 0.9004 (p) REVERT: D 152 ASP cc_start: 0.8385 (m-30) cc_final: 0.7934 (t0) REVERT: E 164 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7165 (tttm) REVERT: E 208 ASP cc_start: 0.8358 (t70) cc_final: 0.8111 (t70) REVERT: F 205 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7709 (mtpp) REVERT: F 208 ASP cc_start: 0.8402 (m-30) cc_final: 0.8089 (t70) REVERT: G 208 ASP cc_start: 0.8329 (m-30) cc_final: 0.8076 (t0) outliers start: 52 outliers final: 35 residues processed: 224 average time/residue: 0.1344 time to fit residues: 48.0730 Evaluate side-chains 217 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 293 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 74 optimal weight: 0.8980 chunk 158 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 ASN E 17 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.116301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.091430 restraints weight = 29339.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.094100 restraints weight = 19954.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.095924 restraints weight = 15326.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.097278 restraints weight = 12757.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.097963 restraints weight = 11206.176| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16779 Z= 0.169 Angle : 0.459 3.594 22715 Z= 0.255 Chirality : 0.046 0.139 2429 Planarity : 0.002 0.022 2933 Dihedral : 4.489 44.310 2228 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.87 % Allowed : 13.40 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.18), residues: 2037 helix: None (None), residues: 0 sheet: -0.05 (0.15), residues: 1127 loop : -0.49 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 56 TYR 0.012 0.001 TYR D 148 PHE 0.010 0.001 PHE D 84 TRP 0.011 0.001 TRP G 260 HIS 0.003 0.001 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (16779) covalent geometry : angle 0.45877 / 0.26 (22715) hydrogen bonds : bond 0.03022 / 1.99 ( 699) hydrogen bonds : angle 5.65916 / 3.93 ( 1899) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.8067 (m-30) cc_final: 0.7855 (t0) REVERT: A 208 ASP cc_start: 0.8312 (t0) cc_final: 0.7829 (t0) REVERT: B 3 SER cc_start: 0.9444 (p) cc_final: 0.9201 (t) REVERT: B 204 MET cc_start: 0.7949 (pmm) cc_final: 0.7570 (pmm) REVERT: B 264 ASN cc_start: 0.8926 (p0) cc_final: 0.8704 (p0) REVERT: D 21 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7798 (ttmt) REVERT: D 76 SER cc_start: 0.9275 (t) cc_final: 0.8997 (p) REVERT: D 152 ASP cc_start: 0.8318 (m-30) cc_final: 0.7907 (t0) REVERT: E 164 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7225 (tttm) REVERT: E 208 ASP cc_start: 0.8291 (t70) cc_final: 0.8061 (t70) REVERT: F 205 LYS cc_start: 0.8218 (mtmm) cc_final: 0.7825 (mtpp) REVERT: F 208 ASP cc_start: 0.8296 (m-30) cc_final: 0.8096 (t0) REVERT: G 65 TYR cc_start: 0.8809 (t80) cc_final: 0.8605 (t80) outliers start: 52 outliers final: 37 residues processed: 214 average time/residue: 0.1353 time to fit residues: 46.7930 Evaluate side-chains 220 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 259 HIS Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 293 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 44 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.116731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.093174 restraints weight = 29207.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.094150 restraints weight = 23061.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.095296 restraints weight = 18720.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.095994 restraints weight = 16068.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.096145 restraints weight = 13995.217| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16779 Z= 0.151 Angle : 0.438 3.510 22715 Z= 0.244 Chirality : 0.045 0.141 2429 Planarity : 0.002 0.020 2933 Dihedral : 4.232 41.998 2225 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.70 % Allowed : 14.12 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.18), residues: 2037 helix: None (None), residues: 0 sheet: -0.01 (0.15), residues: 1127 loop : -0.41 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 56 TYR 0.012 0.001 TYR G 65 PHE 0.010 0.001 PHE D 84 TRP 0.008 0.001 TRP G 260 HIS 0.003 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (16779) covalent geometry : angle 0.43823 / 0.24 (22715) hydrogen bonds : bond 0.02777 / 1.84 ( 699) hydrogen bonds : angle 5.37196 / 3.73 ( 1899) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ASP cc_start: 0.8423 (t0) cc_final: 0.7942 (t0) REVERT: B 3 SER cc_start: 0.9427 (p) cc_final: 0.9189 (t) REVERT: B 204 MET cc_start: 0.7898 (pmm) cc_final: 0.7508 (pmm) REVERT: B 264 ASN cc_start: 0.8904 (p0) cc_final: 0.8696 (p0) REVERT: C 5 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7690 (mt) REVERT: C 208 ASP cc_start: 0.8243 (t0) cc_final: 0.7637 (t0) REVERT: D 21 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7776 (ttmt) REVERT: D 76 SER cc_start: 0.9320 (t) cc_final: 0.9022 (p) REVERT: D 152 ASP cc_start: 0.8260 (m-30) cc_final: 0.7922 (t0) REVERT: E 164 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7270 (tttm) REVERT: E 208 ASP cc_start: 0.8422 (t70) cc_final: 0.7985 (t0) REVERT: F 205 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7789 (mtpp) outliers start: 49 outliers final: 38 residues processed: 209 average time/residue: 0.1332 time to fit residues: 45.4277 Evaluate side-chains 219 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 259 HIS Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 293 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 107 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 chunk 145 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.115904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.091012 restraints weight = 29244.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.093649 restraints weight = 19974.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.095367 restraints weight = 15308.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.096706 restraints weight = 12841.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.097380 restraints weight = 11476.227| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16779 Z= 0.182 Angle : 0.461 3.589 22715 Z= 0.256 Chirality : 0.045 0.139 2429 Planarity : 0.002 0.023 2933 Dihedral : 4.322 41.774 2225 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.03 % Allowed : 15.06 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.18), residues: 2037 helix: None (None), residues: 0 sheet: -0.04 (0.15), residues: 1127 loop : -0.46 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 56 TYR 0.014 0.002 TYR G 65 PHE 0.011 0.001 PHE D 84 TRP 0.008 0.001 TRP G 260 HIS 0.003 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (16779) covalent geometry : angle 0.46115 / 0.26 (22715) hydrogen bonds : bond 0.02879 / 1.91 ( 699) hydrogen bonds : angle 5.34524 / 3.71 ( 1899) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ASP cc_start: 0.8367 (t0) cc_final: 0.8149 (t0) REVERT: B 3 SER cc_start: 0.9411 (p) cc_final: 0.9192 (t) REVERT: B 204 MET cc_start: 0.8066 (pmm) cc_final: 0.7743 (pmm) REVERT: B 264 ASN cc_start: 0.8877 (p0) cc_final: 0.8662 (p0) REVERT: C 5 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7738 (mt) REVERT: C 208 ASP cc_start: 0.8248 (t0) cc_final: 0.7693 (t0) REVERT: D 76 SER cc_start: 0.9283 (t) cc_final: 0.8981 (p) REVERT: D 152 ASP cc_start: 0.8291 (m-30) cc_final: 0.7921 (t0) REVERT: E 21 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7852 (ttmt) REVERT: E 164 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7325 (tttm) REVERT: E 201 ASN cc_start: 0.8937 (p0) cc_final: 0.8710 (p0) REVERT: E 208 ASP cc_start: 0.8356 (t70) cc_final: 0.7945 (t0) REVERT: F 205 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7922 (mtpp) REVERT: F 208 ASP cc_start: 0.8234 (t0) cc_final: 0.7816 (t0) outliers start: 55 outliers final: 42 residues processed: 212 average time/residue: 0.1355 time to fit residues: 46.7820 Evaluate side-chains 222 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 21 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 293 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 5 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 201 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.112669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.088592 restraints weight = 30224.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.090248 restraints weight = 24278.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.091128 restraints weight = 18219.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.091316 restraints weight = 16259.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.091470 restraints weight = 15687.853| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 16779 Z= 0.375 Angle : 0.638 5.079 22715 Z= 0.353 Chirality : 0.051 0.145 2429 Planarity : 0.004 0.041 2933 Dihedral : 5.097 46.812 2225 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.25 % Allowed : 15.44 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.18), residues: 2037 helix: None (None), residues: 0 sheet: -0.41 (0.15), residues: 1127 loop : -0.89 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 253 TYR 0.023 0.003 TYR C 148 PHE 0.019 0.003 PHE D 84 TRP 0.013 0.002 TRP E 260 HIS 0.006 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00904 / 0.37 (16779) covalent geometry : angle 0.63846 / 0.35 (22715) hydrogen bonds : bond 0.03720 / 2.46 ( 699) hydrogen bonds : angle 5.76616 / 3.99 ( 1899) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 196 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ASP cc_start: 0.8507 (t0) cc_final: 0.8003 (t0) REVERT: B 3 SER cc_start: 0.9433 (p) cc_final: 0.9213 (t) REVERT: B 265 TRP cc_start: 0.9506 (m100) cc_final: 0.8820 (m100) REVERT: C 5 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7927 (mt) REVERT: C 162 ASP cc_start: 0.8761 (p0) cc_final: 0.8514 (p0) REVERT: C 208 ASP cc_start: 0.8431 (t0) cc_final: 0.8203 (t0) REVERT: D 75 LYS cc_start: 0.7516 (tttt) cc_final: 0.7297 (ttmm) REVERT: D 205 LYS cc_start: 0.8022 (mtmm) cc_final: 0.7596 (mtpp) REVERT: E 8 LYS cc_start: 0.8026 (tttt) cc_final: 0.7690 (ttmt) REVERT: E 21 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7940 (ttmm) REVERT: E 164 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7463 (tttm) REVERT: E 201 ASN cc_start: 0.8999 (p0) cc_final: 0.8792 (p0) REVERT: E 208 ASP cc_start: 0.8526 (t70) cc_final: 0.8155 (t0) REVERT: F 164 LYS cc_start: 0.8314 (pttt) cc_final: 0.7848 (pptt) REVERT: F 208 ASP cc_start: 0.8408 (t0) cc_final: 0.8054 (t70) REVERT: G 8 LYS cc_start: 0.7974 (tttt) cc_final: 0.7758 (ttmm) REVERT: G 101 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8741 (p90) REVERT: G 113 MET cc_start: 0.7704 (mtp) cc_final: 0.7298 (mtt) outliers start: 59 outliers final: 44 residues processed: 229 average time/residue: 0.1543 time to fit residues: 54.2235 Evaluate side-chains 240 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 148 TYR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 21 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 293 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 157 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.119415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.091358 restraints weight = 29168.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.094759 restraints weight = 17986.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.096982 restraints weight = 13105.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.098451 restraints weight = 10620.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.099587 restraints weight = 9213.772| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16779 Z= 0.107 Angle : 0.432 3.578 22715 Z= 0.240 Chirality : 0.044 0.141 2429 Planarity : 0.002 0.029 2933 Dihedral : 4.366 41.448 2225 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.10 % Allowed : 16.33 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.18), residues: 2037 helix: None (None), residues: 0 sheet: -0.15 (0.15), residues: 1113 loop : -0.62 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 56 TYR 0.015 0.001 TYR G 65 PHE 0.007 0.001 PHE D 224 TRP 0.008 0.001 TRP G 260 HIS 0.003 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (16779) covalent geometry : angle 0.43244 / 0.24 (22715) hydrogen bonds : bond 0.02568 / 1.71 ( 699) hydrogen bonds : angle 5.34559 / 3.71 ( 1899) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 ASP cc_start: 0.8450 (t0) cc_final: 0.7926 (t0) REVERT: B 3 SER cc_start: 0.9404 (p) cc_final: 0.9196 (t) REVERT: B 265 TRP cc_start: 0.9464 (m100) cc_final: 0.8973 (m100) REVERT: C 208 ASP cc_start: 0.8329 (t0) cc_final: 0.8100 (t0) REVERT: D 75 LYS cc_start: 0.7634 (tttt) cc_final: 0.7401 (ttmm) REVERT: D 152 ASP cc_start: 0.8288 (m-30) cc_final: 0.7880 (t0) REVERT: D 205 LYS cc_start: 0.7982 (mtmm) cc_final: 0.7546 (mtpp) REVERT: E 21 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7760 (ttmt) REVERT: E 164 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7267 (tttm) REVERT: E 201 ASN cc_start: 0.8941 (p0) cc_final: 0.8710 (p0) REVERT: E 208 ASP cc_start: 0.8419 (t70) cc_final: 0.8044 (t0) REVERT: F 208 ASP cc_start: 0.8359 (t0) cc_final: 0.8002 (t70) REVERT: G 113 MET cc_start: 0.7536 (mtp) cc_final: 0.7065 (mtt) outliers start: 38 outliers final: 30 residues processed: 209 average time/residue: 0.1412 time to fit residues: 46.3814 Evaluate side-chains 215 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 21 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 293 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 3.9990 chunk 115 optimal weight: 0.0010 chunk 113 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.091542 restraints weight = 29065.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.094906 restraints weight = 17921.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.097223 restraints weight = 12950.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.098837 restraints weight = 10397.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.099679 restraints weight = 9051.939| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16779 Z= 0.119 Angle : 0.426 3.632 22715 Z= 0.237 Chirality : 0.044 0.141 2429 Planarity : 0.002 0.029 2933 Dihedral : 4.178 39.799 2225 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.26 % Allowed : 16.66 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.18), residues: 2037 helix: None (None), residues: 0 sheet: -0.08 (0.15), residues: 1127 loop : -0.48 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.015 0.001 TYR G 65 PHE 0.008 0.001 PHE D 84 TRP 0.007 0.001 TRP F 167 HIS 0.003 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (16779) covalent geometry : angle 0.42591 / 0.24 (22715) hydrogen bonds : bond 0.02539 / 1.69 ( 699) hydrogen bonds : angle 5.16700 / 3.58 ( 1899) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 ASP cc_start: 0.8486 (t0) cc_final: 0.7954 (t0) REVERT: B 3 SER cc_start: 0.9391 (p) cc_final: 0.9173 (t) REVERT: B 265 TRP cc_start: 0.9460 (m100) cc_final: 0.8930 (m100) REVERT: C 208 ASP cc_start: 0.8394 (t0) cc_final: 0.8174 (t0) REVERT: D 75 LYS cc_start: 0.7606 (tttt) cc_final: 0.7347 (ttmm) REVERT: D 152 ASP cc_start: 0.8263 (m-30) cc_final: 0.7871 (t0) REVERT: D 205 LYS cc_start: 0.7927 (mtmm) cc_final: 0.7474 (mtpp) REVERT: E 21 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7694 (ttmt) REVERT: E 164 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7298 (tttm) REVERT: E 201 ASN cc_start: 0.8925 (p0) cc_final: 0.8632 (p0) REVERT: E 208 ASP cc_start: 0.8454 (t70) cc_final: 0.8078 (t0) REVERT: F 164 LYS cc_start: 0.8239 (pttt) cc_final: 0.7759 (pptt) REVERT: F 208 ASP cc_start: 0.8450 (t0) cc_final: 0.8118 (t70) outliers start: 41 outliers final: 36 residues processed: 210 average time/residue: 0.1370 time to fit residues: 46.2907 Evaluate side-chains 224 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 21 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 293 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 113 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.117673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.089666 restraints weight = 29515.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.092959 restraints weight = 18360.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.095279 restraints weight = 13314.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.096668 restraints weight = 10836.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.097714 restraints weight = 9445.985| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 16779 Z= 0.216 Angle : 0.491 3.628 22715 Z= 0.272 Chirality : 0.046 0.140 2429 Planarity : 0.003 0.031 2933 Dihedral : 4.406 40.871 2225 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.21 % Allowed : 16.88 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.18), residues: 2037 helix: None (None), residues: 0 sheet: -0.15 (0.15), residues: 1127 loop : -0.60 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 200 TYR 0.015 0.002 TYR C 148 PHE 0.013 0.002 PHE D 84 TRP 0.009 0.001 TRP E 260 HIS 0.004 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (16779) covalent geometry : angle 0.49125 / 0.27 (22715) hydrogen bonds : bond 0.02888 / 1.92 ( 699) hydrogen bonds : angle 5.26961 / 3.65 ( 1899) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 1 is missing expected H atoms. Skipping. Residue ILE 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue THR 9 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 62 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue ALA 79 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue MET 197 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 204 is missing expected H atoms. Skipping. Residue ALA 206 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ALA 238 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue VAL 247 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue THR 261 is missing expected H atoms. Skipping. Residue THR 263 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 ASP cc_start: 0.8501 (t0) cc_final: 0.7993 (t0) REVERT: B 3 SER cc_start: 0.9396 (p) cc_final: 0.9191 (t) REVERT: B 265 TRP cc_start: 0.9394 (m100) cc_final: 0.9070 (m100) REVERT: C 208 ASP cc_start: 0.8418 (t0) cc_final: 0.8214 (t0) REVERT: D 152 ASP cc_start: 0.8309 (m-30) cc_final: 0.7887 (t0) REVERT: D 205 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7543 (mtpp) REVERT: E 21 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7776 (ttmm) REVERT: E 164 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7388 (tttm) REVERT: E 201 ASN cc_start: 0.8945 (p0) cc_final: 0.8665 (p0) REVERT: E 208 ASP cc_start: 0.8466 (t70) cc_final: 0.8092 (t0) REVERT: F 164 LYS cc_start: 0.8299 (pttt) cc_final: 0.7774 (pptt) REVERT: F 208 ASP cc_start: 0.8443 (t0) cc_final: 0.8119 (t70) outliers start: 40 outliers final: 33 residues processed: 213 average time/residue: 0.1332 time to fit residues: 45.1584 Evaluate side-chains 222 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 21 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 293 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 33 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 20 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.118870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.091688 restraints weight = 29273.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.094859 restraints weight = 18754.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.097018 restraints weight = 13841.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.098357 restraints weight = 11355.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.099336 restraints weight = 9940.287| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16779 Z= 0.145 Angle : 0.445 3.951 22715 Z= 0.247 Chirality : 0.045 0.148 2429 Planarity : 0.002 0.031 2933 Dihedral : 4.237 38.846 2225 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.15 % Allowed : 16.93 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 2037 helix: None (None), residues: 0 sheet: -0.16 (0.15), residues: 1141 loop : -0.50 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 104 TYR 0.014 0.001 TYR G 65 PHE 0.009 0.001 PHE D 84 TRP 0.008 0.001 TRP E 260 HIS 0.003 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 (16779) covalent geometry : angle 0.44489 / 0.25 (22715) hydrogen bonds : bond 0.02620 / 1.74 ( 699) hydrogen bonds : angle 5.17788 / 3.59 ( 1899) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2556.46 seconds wall clock time: 45 minutes 22.32 seconds (2722.32 seconds total)