Starting phenix.real_space_refine on Sun Sep 13 01:27:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21gg_67648/09_2026/21gg_67648.cif Found real_map, /net/cci-nas-00/data/ceres_data/21gg_67648/09_2026/21gg_67648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21gg_67648/09_2026/21gg_67648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21gg_67648/09_2026/21gg_67648.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21gg_67648/09_2026/21gg_67648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21gg_67648/09_2026/21gg_67648.map" } resolution = 4.1 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= 0.003 sd= 0.046 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 9772 2.51 5 N 2653 2.21 5 O 3066 1.98 5 H 3811 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 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: 19351 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2772 Classifications: {'peptide': 274} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 264} Chain breaks: 1 Chain: "B" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2756 Classifications: {'peptide': 274} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 264} Chain breaks: 1 Chain: "C" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2756 Classifications: {'peptide': 274} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 264} Chain breaks: 1 Chain: "D" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2775 Classifications: {'peptide': 274} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 264} Chain breaks: 1 Chain: "E" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2758 Classifications: {'peptide': 274} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 264} Chain breaks: 1 Chain: "F" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2767 Classifications: {'peptide': 274} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 264} Chain breaks: 1 Chain: "G" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2767 Classifications: {'peptide': 274} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 264} Chain breaks: 1 Time building chain proxies: 4.10, per 1000 atoms: 0.21 Number of scatterers: 19351 At special positions: 0 Unit cell: (111.32, 112.24, 92, 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 3066 8.00 N 2653 7.00 C 9772 6.00 H 3811 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: 1.53 Conformation dependent library (CDL) restraints added in 749.7 milliseconds 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3626 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 36 sheets defined 7.7% alpha, 64.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 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 'A' and resid 217 through 222 removed outlier: 4.409A pdb=" N SER A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 6 removed outlier: 3.538A 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: 4.361A pdb=" N SER B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 removed outlier: 3.534A pdb=" N ASN C 6 " --> pdb=" O SER C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 212 through 216 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 'D' and resid 218 through 222 removed outlier: 3.525A pdb=" N SER D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 218 through 222' Processing helix chain 'E' and resid 1 through 6 removed outlier: 3.531A pdb=" N ASN E 6 " --> pdb=" O SER E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 212 through 216 Processing helix chain 'E' and resid 217 through 222 removed outlier: 4.411A pdb=" N SER E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 6 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 Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' 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: 4.389A pdb=" N SER G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 29 removed outlier: 3.714A pdb=" N LYS A 21 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 34 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A 234 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP A 100 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR A 233 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE A 98 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 29 removed outlier: 3.714A pdb=" N LYS A 21 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 34 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 70 removed outlier: 5.619A pdb=" N VAL A 67 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA A 79 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 69 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 86 " --> pdb=" O TRP A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 70 removed outlier: 5.619A pdb=" N VAL A 67 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA A 79 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 69 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS A 75 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N TRP A 260 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLY A 77 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A 258 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA A 79 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TYR A 256 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASP A 254 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 250 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR A 243 " --> pdb=" O TYR A 282 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR A 282 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE A 245 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLU A 280 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 247 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER A 278 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR A 249 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASP A 276 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG A 251 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP A 274 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG A 253 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP A 272 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS A 259 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 290 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 111 through 118 removed outlier: 3.600A pdb=" N THR G 115 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR E 115 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 142 " --> pdb=" O TYR B 118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR C 148 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 115 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 142 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 174 through 176 removed outlier: 7.322A pdb=" N ASN A 176 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLY A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 22 through 29 removed outlier: 3.721A pdb=" N MET B 234 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 229 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TYR B 101 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 231 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 22 through 29 Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 70 removed outlier: 5.936A pdb=" N VAL B 67 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA B 79 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N SER B 82 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 171 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 86 " --> pdb=" O TRP B 167 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 170 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 70 removed outlier: 5.936A pdb=" N VAL B 67 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA B 79 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP B 80 " --> pdb=" O ASP B 254 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 252 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE B 84 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU B 250 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 86 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE B 248 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU B 88 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASP B 246 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B 249 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASP B 255 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASP B 272 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLN B 257 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N THR B 270 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N HIS B 259 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR B 268 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 174 through 176 removed outlier: 7.447A pdb=" N ASN B 176 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLY B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 21 through 29 removed outlier: 3.754A pdb=" N LYS C 21 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET C 34 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA C 229 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N TYR C 101 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C 231 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 21 through 29 removed outlier: 3.754A pdb=" N LYS C 21 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET C 34 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.643A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU C 70 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LYS C 75 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N SER C 82 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE C 171 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 86 " --> pdb=" O TRP C 167 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.643A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU C 70 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LYS C 75 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TRP C 80 " --> pdb=" O ASP C 254 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL C 252 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE C 84 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU C 250 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL C 86 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 248 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU C 88 " --> pdb=" O ASP C 246 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP C 246 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ASP C 255 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ASP C 272 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLN C 257 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR C 270 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N HIS C 259 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N THR C 268 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 285 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU C 290 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 174 through 176 removed outlier: 7.240A pdb=" N ASN C 176 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLY C 180 " --> pdb=" O ASN C 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 21 through 29 removed outlier: 3.586A pdb=" N LYS D 21 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 37 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D 228 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP D 100 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR D 233 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE D 98 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 21 through 29 removed outlier: 3.586A pdb=" N LYS D 21 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 37 " --> pdb=" O LYS D 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 66 through 71 removed outlier: 3.617A pdb=" N ARG D 66 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY D 77 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLU D 70 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LYS D 75 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N SER D 82 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE D 171 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL D 86 " --> pdb=" O TRP D 167 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D 170 " --> pdb=" O LYS D 154 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 66 through 71 removed outlier: 3.617A pdb=" N ARG D 66 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY D 77 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLU D 70 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LYS D 75 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS D 75 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N TRP D 260 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLY D 77 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU D 258 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALA D 79 " --> pdb=" O TYR D 256 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N TYR D 256 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP D 254 " --> pdb=" O PRO D 81 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ASP D 255 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASP D 272 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLN D 257 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N THR D 270 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N HIS D 259 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N THR D 268 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU D 290 " --> pdb=" O ASP D 285 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 174 through 176 removed outlier: 6.329A pdb=" N MET D 174 " --> pdb=" O PRO D 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 21 through 29 removed outlier: 3.666A pdb=" N LYS E 21 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET E 34 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ALA E 229 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR E 101 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL E 231 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 21 through 29 removed outlier: 3.666A pdb=" N LYS E 21 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET E 34 " --> pdb=" O ASP E 29 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 66 through 70 removed outlier: 3.825A pdb=" N ARG E 66 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU E 70 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS E 75 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N SER E 82 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE E 171 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL E 86 " --> pdb=" O TRP E 167 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 66 through 70 removed outlier: 3.825A pdb=" N ARG E 66 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU E 70 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS E 75 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP E 80 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL E 252 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE E 84 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU E 250 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL E 86 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE E 248 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU E 88 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP E 246 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR E 249 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASP E 255 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASP E 272 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLN E 257 " --> pdb=" O THR E 270 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N THR E 270 " --> pdb=" O GLN E 257 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N HIS E 259 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N THR E 268 " --> pdb=" O HIS E 259 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU E 290 " --> pdb=" O ASP E 285 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 174 through 176 removed outlier: 7.387A pdb=" N ASN E 176 " --> pdb=" O GLY E 180 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY E 180 " --> pdb=" O ASN E 176 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 21 through 29 removed outlier: 3.599A pdb=" N LYS F 21 " --> pdb=" O PHE F 42 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET F 34 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET F 234 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE F 228 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ALA F 229 " --> pdb=" O TYR F 101 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR F 101 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL F 231 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 21 through 29 removed outlier: 3.599A pdb=" N LYS F 21 " --> pdb=" O PHE F 42 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET F 34 " --> pdb=" O ASP F 29 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 66 through 70 removed outlier: 5.898A pdb=" N VAL F 67 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA F 79 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER F 69 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N SER F 82 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F 86 " --> pdb=" O TRP F 167 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 66 through 70 removed outlier: 5.898A pdb=" N VAL F 67 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA F 79 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER F 69 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS F 75 " --> pdb=" O TRP F 260 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N TRP F 260 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLY F 77 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU F 258 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ALA F 79 " --> pdb=" O TYR F 256 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR F 256 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASP F 254 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE F 248 " --> pdb=" O GLN F 87 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR F 249 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASP F 255 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP F 272 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N GLN F 257 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N THR F 270 " --> pdb=" O GLN F 257 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N HIS F 259 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR F 268 " --> pdb=" O HIS F 259 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU F 290 " --> pdb=" O ASP F 285 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 174 through 176 removed outlier: 7.545A pdb=" N ASN F 176 " --> pdb=" O GLY F 180 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLY F 180 " --> pdb=" O ASN F 176 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 21 through 29 removed outlier: 3.698A pdb=" N LYS G 21 " --> pdb=" O PHE G 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET G 234 " --> pdb=" O LYS G 51 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP G 100 " --> pdb=" O VAL G 231 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR G 233 " --> pdb=" O ILE G 98 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE G 98 " --> pdb=" O THR G 233 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 21 through 29 removed outlier: 3.698A pdb=" N LYS G 21 " --> pdb=" O PHE G 42 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.540A pdb=" N ARG G 66 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY G 77 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU G 70 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS G 75 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL G 86 " --> pdb=" O TRP G 167 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.540A pdb=" N ARG G 66 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY G 77 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU G 70 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS G 75 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LYS G 75 " --> pdb=" O TRP G 260 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N TRP G 260 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY G 77 " --> pdb=" O LEU G 258 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU G 258 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ALA G 79 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TYR G 256 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP G 254 " --> pdb=" O PRO G 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU G 250 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASP G 255 " --> pdb=" O ASP G 272 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASP G 272 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLN G 257 " --> pdb=" O THR G 270 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N THR G 270 " --> pdb=" O GLN G 257 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N HIS G 259 " --> pdb=" O THR G 268 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR G 268 " --> pdb=" O HIS G 259 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU G 290 " --> pdb=" O ASP G 285 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 174 through 176 removed outlier: 7.361A pdb=" N ASN G 176 " --> pdb=" O GLY G 180 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLY G 180 " --> pdb=" O ASN G 176 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 1926 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: 3.53 Time building geometry restraints manager: 2.10 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: 3811 1.03 - 1.22: 3 1.22 - 1.42: 6836 1.42 - 1.61: 8953 1.61 - 1.81: 98 Bond restraints: 19701 Sorted by residual: bond pdb=" C TRP B 80 " pdb=" N PRO B 81 " ideal model delta sigma weight residual 1.335 1.317 0.018 8.70e-03 1.32e+04 4.22e+00 bond pdb=" C TRP D 80 " pdb=" N PRO D 81 " ideal model delta sigma weight residual 1.333 1.316 0.017 1.01e-02 9.80e+03 3.00e+00 bond pdb=" C LYS E 58 " pdb=" N GLY E 59 " ideal model delta sigma weight residual 1.335 1.322 0.012 7.50e-03 1.78e+04 2.69e+00 bond pdb=" C GLN B 89 " pdb=" N LEU B 90 " ideal model delta sigma weight residual 1.329 1.302 0.027 1.86e-02 2.89e+03 2.09e+00 bond pdb=" CA LEU A 53 " pdb=" C LEU A 53 " ideal model delta sigma weight residual 1.530 1.518 0.013 1.08e-02 8.57e+03 1.41e+00 ... (remaining 19696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 27440 1.27 - 2.53: 813 2.53 - 3.80: 96 3.80 - 5.06: 11 5.06 - 6.33: 4 Bond angle restraints: 28364 Sorted by residual: angle pdb=" N SER A 262 " pdb=" CA SER A 262 " pdb=" CB SER A 262 " ideal model delta sigma weight residual 114.17 110.43 3.74 1.14e+00 7.69e-01 1.08e+01 angle pdb=" N SER B 262 " pdb=" CA SER B 262 " pdb=" CB SER B 262 " ideal model delta sigma weight residual 114.17 110.51 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N ILE C 5 " pdb=" CA ILE C 5 " pdb=" C ILE C 5 " ideal model delta sigma weight residual 111.91 109.11 2.80 8.90e-01 1.26e+00 9.92e+00 angle pdb=" N GLY F 143 " pdb=" CA GLY F 143 " pdb=" C GLY F 143 " ideal model delta sigma weight residual 110.96 115.32 -4.36 1.49e+00 4.50e-01 8.56e+00 angle pdb=" N ILE E 5 " pdb=" CA ILE E 5 " pdb=" C ILE E 5 " ideal model delta sigma weight residual 111.91 109.32 2.59 8.90e-01 1.26e+00 8.45e+00 ... (remaining 28359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 11571 17.91 - 35.81: 637 35.81 - 53.72: 103 53.72 - 71.63: 32 71.63 - 89.53: 12 Dihedral angle restraints: 12355 sinusoidal: 6629 harmonic: 5726 Sorted by residual: dihedral pdb=" CA GLU C 289 " pdb=" C GLU C 289 " pdb=" N GLU C 290 " pdb=" CA GLU C 290 " ideal model delta harmonic sigma weight residual 180.00 162.30 17.70 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CG ARG G 253 " pdb=" CD ARG G 253 " pdb=" NE ARG G 253 " pdb=" CZ ARG G 253 " ideal model delta sinusoidal sigma weight residual -90.00 -134.82 44.82 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB LYS F 8 " pdb=" CG LYS F 8 " pdb=" CD LYS F 8 " pdb=" CE LYS F 8 " ideal model delta sinusoidal sigma weight residual 60.00 113.13 -53.13 3 1.50e+01 4.44e-03 9.18e+00 ... (remaining 12352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1334 0.029 - 0.057: 598 0.057 - 0.086: 177 0.086 - 0.114: 158 0.114 - 0.143: 36 Chirality restraints: 2303 Sorted by residual: chirality pdb=" CA ILE C 142 " pdb=" N ILE C 142 " pdb=" C ILE C 142 " pdb=" CB ILE C 142 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA PRO G 189 " pdb=" N PRO G 189 " pdb=" C PRO G 189 " pdb=" CB PRO G 189 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE G 61 " pdb=" N ILE G 61 " pdb=" C ILE G 61 " pdb=" CB ILE G 61 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 2300 not shown) Planarity restraints: 4599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 71 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" CD GLU A 71 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU A 71 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU A 71 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 179 " -0.011 2.00e-02 2.50e+03 8.01e-03 1.77e+00 pdb=" CG TRP D 179 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP D 179 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP D 179 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 179 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 179 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 179 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 179 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 179 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 179 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TRP D 179 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 185 " 0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" CG ASP E 185 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASP E 185 " 0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP E 185 " 0.007 2.00e-02 2.50e+03 ... (remaining 4596 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.39: 1138 2.39 - 2.94: 19153 2.94 - 3.49: 27865 3.49 - 4.05: 41219 4.05 - 4.60: 54979 Nonbonded interactions: 144354 Sorted by model distance: nonbonded pdb="HH22 ARG D 104 " pdb=" HZ2 LYS E 58 " model vdw 1.832 2.100 nonbonded pdb=" HZ1 LYS F 36 " pdb=" HG SER F 278 " model vdw 1.848 2.100 nonbonded pdb="HD22 ASN F 105 " pdb=" H LEU F 157 " model vdw 1.872 2.100 nonbonded pdb=" HD1 HIS C 48 " pdb=" HG1 THR D 22 " model vdw 1.891 2.100 nonbonded pdb=" H ASP B 183 " pdb=" HG SER B 186 " model vdw 1.894 2.100 ... (remaining 144349 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: 1.700 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: 0.170 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.810 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 0.034 15890 Z= 0.205 Angle : 0.568 6.330 21511 Z= 0.337 Chirality : 0.043 0.143 2303 Planarity : 0.003 0.029 2758 Dihedral : 12.621 89.535 5873 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 28.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -0.64 (0.19), residues: 1890 helix: None (None), residues: 0 sheet: -0.14 (0.16), residues: 1043 loop : -0.66 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 251 TYR 0.016 0.002 TYR D 249 PHE 0.015 0.001 PHE D 224 TRP 0.023 0.001 TRP D 179 HIS 0.005 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 (15890) covalent geometry : angle 0.56805 / 0.34 (21511) hydrogen bonds : bond 0.29603 / 19.72 ( 595) hydrogen bonds : angle 10.54945 / 7.14 ( 1926) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 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 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 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 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 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 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 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 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 376 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ASN cc_start: 0.9183 (m110) cc_final: 0.8838 (m110) REVERT: A 197 MET cc_start: 0.7806 (ttp) cc_final: 0.7556 (ptm) REVERT: A 209 ASN cc_start: 0.8474 (t0) cc_final: 0.8161 (t0) REVERT: A 234 MET cc_start: 0.8789 (tpp) cc_final: 0.8569 (tpp) REVERT: A 253 ARG cc_start: 0.9022 (mtm110) cc_final: 0.8647 (ptp90) REVERT: A 259 HIS cc_start: 0.7798 (p-80) cc_final: 0.7537 (p-80) REVERT: B 3 SER cc_start: 0.9458 (p) cc_final: 0.8975 (t) REVERT: B 204 MET cc_start: 0.6718 (ttp) cc_final: 0.6439 (ttp) REVERT: B 208 ASP cc_start: 0.8020 (m-30) cc_final: 0.7799 (t0) REVERT: C 11 THR cc_start: 0.9200 (m) cc_final: 0.8975 (m) REVERT: C 25 LEU cc_start: 0.9184 (mm) cc_final: 0.8851 (mt) REVERT: C 250 GLU cc_start: 0.8527 (tt0) cc_final: 0.8262 (tt0) REVERT: C 290 GLU cc_start: 0.8684 (pm20) cc_final: 0.8283 (pm20) REVERT: C 291 MET cc_start: 0.7893 (mtp) cc_final: 0.7507 (mtp) REVERT: D 3 SER cc_start: 0.9479 (p) cc_final: 0.9152 (t) REVERT: D 30 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7484 (mttm) REVERT: D 53 LEU cc_start: 0.8478 (tp) cc_final: 0.8085 (tt) REVERT: D 64 GLN cc_start: 0.7970 (mt0) cc_final: 0.7667 (mm-40) REVERT: D 188 ASN cc_start: 0.8232 (t0) cc_final: 0.7075 (m-40) REVERT: D 209 ASN cc_start: 0.8508 (t0) cc_final: 0.8037 (t0) REVERT: D 256 TYR cc_start: 0.8170 (t80) cc_final: 0.7852 (t80) REVERT: D 258 LEU cc_start: 0.8938 (mt) cc_final: 0.8702 (mt) REVERT: D 259 HIS cc_start: 0.7057 (p90) cc_final: 0.6732 (p-80) REVERT: E 3 SER cc_start: 0.9474 (p) cc_final: 0.9075 (t) REVERT: E 11 THR cc_start: 0.9133 (m) cc_final: 0.8922 (m) REVERT: E 25 LEU cc_start: 0.8832 (mm) cc_final: 0.8509 (mt) REVERT: E 188 ASN cc_start: 0.8146 (t0) cc_final: 0.7921 (t0) REVERT: E 253 ARG cc_start: 0.8847 (mtm110) cc_final: 0.8571 (ptp-110) REVERT: F 3 SER cc_start: 0.9439 (p) cc_final: 0.8952 (t) REVERT: F 30 LYS cc_start: 0.7861 (ttmm) cc_final: 0.7217 (mttt) REVERT: F 64 GLN cc_start: 0.8104 (mt0) cc_final: 0.7747 (mm-40) REVERT: F 66 ARG cc_start: 0.8295 (ptp90) cc_final: 0.8002 (ptp90) REVERT: F 188 ASN cc_start: 0.8173 (t0) cc_final: 0.7081 (m-40) REVERT: F 197 MET cc_start: 0.7991 (ttp) cc_final: 0.7590 (ptm) REVERT: F 260 TRP cc_start: 0.8446 (t60) cc_final: 0.8174 (t60) REVERT: G 185 ASP cc_start: 0.7760 (t0) cc_final: 0.7448 (t0) REVERT: G 258 LEU cc_start: 0.8678 (mt) cc_final: 0.8383 (mt) REVERT: G 291 MET cc_start: 0.7905 (mtp) cc_final: 0.7632 (mtp) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.1464 time to fit residues: 85.7246 Evaluate side-chains 321 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN F 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.133188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.103615 restraints weight = 35298.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.107096 restraints weight = 23129.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.109799 restraints weight = 17458.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.111328 restraints weight = 14350.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.112606 restraints weight = 12632.098| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15890 Z= 0.196 Angle : 0.532 5.566 21511 Z= 0.296 Chirality : 0.045 0.149 2303 Planarity : 0.003 0.032 2758 Dihedral : 4.731 39.591 2079 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 29.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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 (0.19), residues: 1890 helix: -0.73 (0.80), residues: 42 sheet: 0.26 (0.16), residues: 1022 loop : -0.94 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 251 TYR 0.018 0.002 TYR E 148 PHE 0.013 0.001 PHE F 224 TRP 0.016 0.001 TRP D 179 HIS 0.007 0.002 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (15890) covalent geometry : angle 0.53233 / 0.30 (21511) hydrogen bonds : bond 0.04611 / 2.94 ( 595) hydrogen bonds : angle 6.59773 / 4.48 ( 1926) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 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 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 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 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 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 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 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 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 357 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9210 (mt0) cc_final: 0.8974 (mt0) REVERT: A 178 ASN cc_start: 0.9170 (m110) cc_final: 0.8806 (m110) REVERT: A 209 ASN cc_start: 0.8735 (t0) cc_final: 0.8469 (t0) REVERT: A 258 LEU cc_start: 0.8687 (mp) cc_final: 0.8246 (mm) REVERT: B 3 SER cc_start: 0.9541 (p) cc_final: 0.9097 (t) REVERT: B 98 ILE cc_start: 0.9075 (mt) cc_final: 0.8771 (mm) REVERT: B 204 MET cc_start: 0.6905 (ttp) cc_final: 0.6325 (ttp) REVERT: B 208 ASP cc_start: 0.8378 (m-30) cc_final: 0.8008 (t0) REVERT: C 291 MET cc_start: 0.8032 (mtp) cc_final: 0.7652 (mtp) REVERT: D 11 THR cc_start: 0.9145 (m) cc_final: 0.8934 (m) REVERT: D 64 GLN cc_start: 0.7870 (mt0) cc_final: 0.7637 (mm-40) REVERT: D 188 ASN cc_start: 0.8331 (t0) cc_final: 0.7171 (m-40) REVERT: D 209 ASN cc_start: 0.8568 (t0) cc_final: 0.8088 (t0) REVERT: D 256 TYR cc_start: 0.8109 (t80) cc_final: 0.7893 (t80) REVERT: D 259 HIS cc_start: 0.7227 (p90) cc_final: 0.6881 (p-80) REVERT: E 11 THR cc_start: 0.9109 (m) cc_final: 0.8898 (m) REVERT: E 188 ASN cc_start: 0.8175 (t0) cc_final: 0.7904 (t0) REVERT: E 197 MET cc_start: 0.7938 (ttp) cc_final: 0.7550 (ptm) REVERT: F 30 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7260 (mttt) REVERT: F 64 GLN cc_start: 0.8091 (mt0) cc_final: 0.7698 (mm-40) REVERT: F 66 ARG cc_start: 0.8344 (ptp90) cc_final: 0.8094 (ptp90) REVERT: F 142 ILE cc_start: 0.8169 (mm) cc_final: 0.7796 (pt) REVERT: F 188 ASN cc_start: 0.8229 (t0) cc_final: 0.7146 (m-40) REVERT: F 197 MET cc_start: 0.7857 (ttp) cc_final: 0.7528 (ptm) REVERT: F 260 TRP cc_start: 0.8469 (t60) cc_final: 0.8212 (t60) REVERT: G 178 ASN cc_start: 0.9115 (m-40) cc_final: 0.8849 (m-40) REVERT: G 185 ASP cc_start: 0.7934 (t0) cc_final: 0.7480 (t0) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.1476 time to fit residues: 82.6819 Evaluate side-chains 300 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 89 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN C 32 ASN ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN F 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.126416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.097272 restraints weight = 36592.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.100490 restraints weight = 25047.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.102704 restraints weight = 19386.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.104204 restraints weight = 16302.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.105166 restraints weight = 14493.181| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 15890 Z= 0.321 Angle : 0.666 10.869 21511 Z= 0.359 Chirality : 0.047 0.148 2303 Planarity : 0.004 0.034 2758 Dihedral : 5.327 28.934 2079 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 33.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % 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: -0.73 (0.19), residues: 1890 helix: None (None), residues: 0 sheet: 0.12 (0.16), residues: 959 loop : -1.12 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 277 TYR 0.028 0.003 TYR E 148 PHE 0.019 0.002 PHE F 153 TRP 0.018 0.002 TRP D 179 HIS 0.007 0.002 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.32 (15890) covalent geometry : angle 0.66619 / 0.36 (21511) hydrogen bonds : bond 0.04921 / 3.19 ( 595) hydrogen bonds : angle 6.21696 / 4.24 ( 1926) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 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 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 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 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 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 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 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 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 334 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9254 (mt0) cc_final: 0.8912 (mt0) REVERT: A 178 ASN cc_start: 0.9192 (m110) cc_final: 0.8852 (m110) REVERT: A 209 ASN cc_start: 0.8814 (t0) cc_final: 0.8418 (t0) REVERT: A 234 MET cc_start: 0.8762 (tpp) cc_final: 0.8548 (tpp) REVERT: A 258 LEU cc_start: 0.8880 (mp) cc_final: 0.8529 (mm) REVERT: B 75 LYS cc_start: 0.7066 (mtmm) cc_final: 0.6853 (mtmm) REVERT: B 204 MET cc_start: 0.7212 (ttp) cc_final: 0.6655 (ttp) REVERT: B 208 ASP cc_start: 0.8469 (m-30) cc_final: 0.8120 (t0) REVERT: B 234 MET cc_start: 0.8426 (tpp) cc_final: 0.8205 (tpt) REVERT: B 260 TRP cc_start: 0.8478 (t60) cc_final: 0.8228 (t60) REVERT: C 291 MET cc_start: 0.7971 (mtp) cc_final: 0.7690 (mtp) REVERT: D 11 THR cc_start: 0.9177 (m) cc_final: 0.8954 (m) REVERT: D 64 GLN cc_start: 0.7900 (mt0) cc_final: 0.7678 (mm-40) REVERT: D 188 ASN cc_start: 0.8445 (t0) cc_final: 0.7347 (m-40) REVERT: D 209 ASN cc_start: 0.8699 (t0) cc_final: 0.8359 (t0) REVERT: D 256 TYR cc_start: 0.8206 (t80) cc_final: 0.7999 (t80) REVERT: D 259 HIS cc_start: 0.7681 (p90) cc_final: 0.7421 (p90) REVERT: E 11 THR cc_start: 0.9267 (m) cc_final: 0.9031 (m) REVERT: E 188 ASN cc_start: 0.8241 (t0) cc_final: 0.8010 (t0) REVERT: E 197 MET cc_start: 0.7946 (ttp) cc_final: 0.7336 (ptm) REVERT: F 64 GLN cc_start: 0.8110 (mt0) cc_final: 0.7817 (mm-40) REVERT: F 142 ILE cc_start: 0.8200 (mm) cc_final: 0.7791 (pt) REVERT: F 188 ASN cc_start: 0.8386 (t0) cc_final: 0.7396 (m-40) REVERT: F 197 MET cc_start: 0.7969 (ttp) cc_final: 0.7654 (ptm) REVERT: F 260 TRP cc_start: 0.8516 (t60) cc_final: 0.8175 (t60) REVERT: G 185 ASP cc_start: 0.8140 (t0) cc_final: 0.7676 (t0) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.1512 time to fit residues: 78.1319 Evaluate side-chains 296 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 124 optimal weight: 0.1980 chunk 69 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 182 optimal weight: 0.0970 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.126683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.102100 restraints weight = 31604.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.104446 restraints weight = 22724.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.106157 restraints weight = 18116.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.107147 restraints weight = 15548.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.107957 restraints weight = 14054.230| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15890 Z= 0.138 Angle : 0.475 4.617 21511 Z= 0.266 Chirality : 0.044 0.147 2303 Planarity : 0.003 0.043 2758 Dihedral : 4.602 19.710 2079 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 29.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: 1890 helix: -0.82 (0.80), residues: 42 sheet: 0.23 (0.16), residues: 924 loop : -0.94 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.015 0.001 TYR D 249 PHE 0.013 0.001 PHE G 42 TRP 0.011 0.001 TRP D 179 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (15890) covalent geometry : angle 0.47542 / 0.27 (21511) hydrogen bonds : bond 0.03502 / 2.22 ( 595) hydrogen bonds : angle 5.60575 / 3.83 ( 1926) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 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 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 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 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 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 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 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 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 362 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8808 (t80) cc_final: 0.8553 (t80) REVERT: A 178 ASN cc_start: 0.9095 (m110) cc_final: 0.8746 (m110) REVERT: A 209 ASN cc_start: 0.8663 (t0) cc_final: 0.8246 (t0) REVERT: A 258 LEU cc_start: 0.8844 (mp) cc_final: 0.8565 (mm) REVERT: B 98 ILE cc_start: 0.8986 (mt) cc_final: 0.8768 (mm) REVERT: B 204 MET cc_start: 0.7008 (ttp) cc_final: 0.6524 (ttp) REVERT: B 260 TRP cc_start: 0.8434 (t60) cc_final: 0.8150 (t60) REVERT: C 253 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.8079 (ptp90) REVERT: D 173 ASN cc_start: 0.8694 (p0) cc_final: 0.8392 (p0) REVERT: D 188 ASN cc_start: 0.8408 (t0) cc_final: 0.7174 (m-40) REVERT: D 209 ASN cc_start: 0.8479 (t0) cc_final: 0.8196 (t0) REVERT: E 11 THR cc_start: 0.9188 (m) cc_final: 0.8963 (m) REVERT: E 253 ARG cc_start: 0.8506 (mtm110) cc_final: 0.8056 (ptm160) REVERT: F 64 GLN cc_start: 0.7875 (mt0) cc_final: 0.7620 (mm-40) REVERT: F 142 ILE cc_start: 0.8213 (mm) cc_final: 0.7933 (pt) REVERT: F 188 ASN cc_start: 0.8239 (t0) cc_final: 0.7176 (m-40) REVERT: F 260 TRP cc_start: 0.8446 (t60) cc_final: 0.7961 (t60) REVERT: G 185 ASP cc_start: 0.7783 (t0) cc_final: 0.7383 (t0) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.1511 time to fit residues: 84.3493 Evaluate side-chains 300 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 66 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 169 optimal weight: 0.0000 chunk 76 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN C 194 GLN ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN F 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.130202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.100878 restraints weight = 35619.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.104185 restraints weight = 24208.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.106456 restraints weight = 18609.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.107945 restraints weight = 15647.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.108900 restraints weight = 13870.723| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15890 Z= 0.196 Angle : 0.522 6.841 21511 Z= 0.287 Chirality : 0.045 0.136 2303 Planarity : 0.003 0.030 2758 Dihedral : 4.647 16.963 2079 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 30.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: -0.55 (0.19), residues: 1890 helix: None (None), residues: 0 sheet: 0.25 (0.17), residues: 924 loop : -0.96 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.031 0.002 TYR C 182 PHE 0.012 0.001 PHE F 224 TRP 0.022 0.001 TRP E 80 HIS 0.008 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (15890) covalent geometry : angle 0.52226 / 0.29 (21511) hydrogen bonds : bond 0.03695 / 2.37 ( 595) hydrogen bonds : angle 5.52365 / 3.77 ( 1926) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 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 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 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 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 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 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 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 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 345 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8818 (t80) cc_final: 0.8467 (t80) REVERT: A 178 ASN cc_start: 0.9145 (m110) cc_final: 0.8861 (m110) REVERT: A 209 ASN cc_start: 0.8903 (t0) cc_final: 0.8529 (t0) REVERT: A 258 LEU cc_start: 0.8547 (mp) cc_final: 0.8234 (mp) REVERT: A 259 HIS cc_start: 0.7673 (p-80) cc_final: 0.7016 (p-80) REVERT: B 204 MET cc_start: 0.7199 (ttp) cc_final: 0.6968 (ttm) REVERT: C 253 ARG cc_start: 0.8371 (mtm-85) cc_final: 0.8043 (ptp90) REVERT: D 11 THR cc_start: 0.9168 (m) cc_final: 0.8926 (m) REVERT: D 173 ASN cc_start: 0.8913 (p0) cc_final: 0.8621 (p0) REVERT: D 188 ASN cc_start: 0.8447 (t0) cc_final: 0.7308 (m-40) REVERT: D 209 ASN cc_start: 0.8718 (t0) cc_final: 0.8406 (t0) REVERT: E 11 THR cc_start: 0.9239 (m) cc_final: 0.9015 (m) REVERT: E 188 ASN cc_start: 0.8269 (t0) cc_final: 0.7916 (t0) REVERT: E 197 MET cc_start: 0.8032 (ttp) cc_final: 0.7601 (ptm) REVERT: E 253 ARG cc_start: 0.8596 (mtm110) cc_final: 0.7997 (ptm160) REVERT: F 64 GLN cc_start: 0.8038 (mt0) cc_final: 0.7761 (mm-40) REVERT: F 142 ILE cc_start: 0.8071 (mm) cc_final: 0.7677 (pt) REVERT: F 173 ASN cc_start: 0.8259 (p0) cc_final: 0.7973 (p0) REVERT: F 188 ASN cc_start: 0.8341 (t0) cc_final: 0.7312 (m-40) REVERT: F 260 TRP cc_start: 0.8516 (t60) cc_final: 0.8039 (t60) REVERT: G 185 ASP cc_start: 0.8131 (t0) cc_final: 0.7627 (t0) REVERT: G 188 ASN cc_start: 0.8550 (t0) cc_final: 0.8312 (t0) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.1498 time to fit residues: 79.9781 Evaluate side-chains 298 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.133540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.103920 restraints weight = 35197.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.107423 restraints weight = 23557.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.109790 restraints weight = 17972.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.111296 restraints weight = 14976.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.112475 restraints weight = 13248.507| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15890 Z= 0.161 Angle : 0.484 6.277 21511 Z= 0.269 Chirality : 0.044 0.140 2303 Planarity : 0.003 0.030 2758 Dihedral : 4.476 16.062 2079 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 30.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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 (0.19), residues: 1890 helix: None (None), residues: 0 sheet: 0.31 (0.17), residues: 924 loop : -0.92 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.023 0.002 TYR A 256 PHE 0.010 0.001 PHE F 224 TRP 0.019 0.001 TRP E 80 HIS 0.006 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (15890) covalent geometry : angle 0.48433 / 0.27 (21511) hydrogen bonds : bond 0.03409 / 2.18 ( 595) hydrogen bonds : angle 5.30830 / 3.63 ( 1926) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 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 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 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 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 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 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 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 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 351 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ASN cc_start: 0.9194 (m110) cc_final: 0.8942 (m110) REVERT: A 209 ASN cc_start: 0.8808 (t0) cc_final: 0.8442 (t0) REVERT: A 258 LEU cc_start: 0.8644 (mp) cc_final: 0.8339 (mp) REVERT: A 259 HIS cc_start: 0.7767 (p-80) cc_final: 0.7011 (p-80) REVERT: B 98 ILE cc_start: 0.9066 (mt) cc_final: 0.8840 (mm) REVERT: B 204 MET cc_start: 0.7212 (ttp) cc_final: 0.7010 (ttm) REVERT: B 260 TRP cc_start: 0.8524 (t60) cc_final: 0.8310 (t60) REVERT: C 253 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7972 (ptp90) REVERT: D 11 THR cc_start: 0.9253 (m) cc_final: 0.9032 (m) REVERT: D 115 THR cc_start: 0.9050 (m) cc_final: 0.8805 (t) REVERT: D 173 ASN cc_start: 0.8900 (p0) cc_final: 0.8626 (p0) REVERT: D 188 ASN cc_start: 0.8584 (t0) cc_final: 0.7313 (m-40) REVERT: E 11 THR cc_start: 0.9242 (m) cc_final: 0.9005 (m) REVERT: E 188 ASN cc_start: 0.8171 (t0) cc_final: 0.7801 (t0) REVERT: E 197 MET cc_start: 0.7984 (ttp) cc_final: 0.7479 (ptm) REVERT: E 253 ARG cc_start: 0.8553 (mtm110) cc_final: 0.8093 (ptm160) REVERT: F 64 GLN cc_start: 0.8031 (mt0) cc_final: 0.7728 (mm-40) REVERT: F 142 ILE cc_start: 0.8125 (mm) cc_final: 0.7709 (pt) REVERT: F 173 ASN cc_start: 0.8240 (p0) cc_final: 0.7938 (p0) REVERT: F 260 TRP cc_start: 0.8533 (t60) cc_final: 0.8088 (t60) REVERT: G 185 ASP cc_start: 0.8058 (t0) cc_final: 0.7556 (t0) REVERT: G 188 ASN cc_start: 0.8575 (t0) cc_final: 0.8327 (t0) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1499 time to fit residues: 81.4842 Evaluate side-chains 299 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 162 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN D 269 ASN F 105 ASN F 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.125894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.097030 restraints weight = 36782.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.100026 restraints weight = 25795.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.102055 restraints weight = 20308.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.103411 restraints weight = 17285.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.104120 restraints weight = 15505.266| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 15890 Z= 0.378 Angle : 0.711 11.385 21511 Z= 0.383 Chirality : 0.048 0.152 2303 Planarity : 0.004 0.037 2758 Dihedral : 5.507 19.313 2079 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 36.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -0.98 (0.19), residues: 1890 helix: None (None), residues: 0 sheet: 0.01 (0.17), residues: 924 loop : -1.32 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 251 TYR 0.027 0.003 TYR A 256 PHE 0.020 0.002 PHE F 153 TRP 0.030 0.002 TRP E 80 HIS 0.005 0.001 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00896 / 0.38 (15890) covalent geometry : angle 0.71106 / 0.38 (21511) hydrogen bonds : bond 0.04665 / 3.02 ( 595) hydrogen bonds : angle 5.87180 / 4.02 ( 1926) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 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 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 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 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 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 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 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 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 323 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.8801 (t0) cc_final: 0.8447 (t0) REVERT: A 234 MET cc_start: 0.8804 (tpp) cc_final: 0.8583 (tpp) REVERT: A 258 LEU cc_start: 0.8858 (mp) cc_final: 0.8505 (mp) REVERT: A 259 HIS cc_start: 0.8153 (p-80) cc_final: 0.7647 (p-80) REVERT: A 290 GLU cc_start: 0.7984 (pt0) cc_final: 0.7756 (pt0) REVERT: A 291 MET cc_start: 0.7887 (mtp) cc_final: 0.7682 (mtp) REVERT: B 234 MET cc_start: 0.8438 (tpp) cc_final: 0.8235 (tpt) REVERT: B 260 TRP cc_start: 0.8595 (t60) cc_final: 0.8348 (t60) REVERT: C 91 PRO cc_start: 0.8733 (Cg_exo) cc_final: 0.8491 (Cg_endo) REVERT: C 234 MET cc_start: 0.8653 (tpp) cc_final: 0.8421 (tpp) REVERT: D 11 THR cc_start: 0.9222 (m) cc_final: 0.8996 (m) REVERT: D 188 ASN cc_start: 0.8637 (t0) cc_final: 0.7518 (m-40) REVERT: E 188 ASN cc_start: 0.8364 (t0) cc_final: 0.8004 (t0) REVERT: E 197 MET cc_start: 0.8162 (ttp) cc_final: 0.7474 (ptm) REVERT: F 64 GLN cc_start: 0.8154 (mt0) cc_final: 0.7836 (mm-40) REVERT: F 142 ILE cc_start: 0.8054 (mm) cc_final: 0.7656 (pt) REVERT: F 188 ASN cc_start: 0.8450 (t0) cc_final: 0.7613 (m-40) REVERT: F 260 TRP cc_start: 0.8505 (t60) cc_final: 0.7984 (t60) REVERT: G 185 ASP cc_start: 0.8294 (t0) cc_final: 0.7783 (t0) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1429 time to fit residues: 73.0452 Evaluate side-chains 284 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 181 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN G 150 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.123093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.098342 restraints weight = 32841.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.100896 restraints weight = 22880.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.102570 restraints weight = 17858.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.103875 restraints weight = 15129.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.104614 restraints weight = 13474.149| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15890 Z= 0.195 Angle : 0.535 6.735 21511 Z= 0.296 Chirality : 0.045 0.135 2303 Planarity : 0.004 0.050 2758 Dihedral : 4.985 18.120 2079 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 32.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -0.89 (0.18), residues: 1890 helix: None (None), residues: 0 sheet: 0.04 (0.17), residues: 924 loop : -1.21 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 253 TYR 0.021 0.002 TYR A 256 PHE 0.014 0.001 PHE F 210 TRP 0.018 0.001 TRP E 80 HIS 0.006 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (15890) covalent geometry : angle 0.53476 / 0.30 (21511) hydrogen bonds : bond 0.03751 / 2.39 ( 595) hydrogen bonds : angle 5.49609 / 3.76 ( 1926) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 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 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 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 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 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 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 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 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 329 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8327 (ttp80) cc_final: 0.7961 (ttp80) REVERT: A 178 ASN cc_start: 0.9304 (m110) cc_final: 0.9004 (m110) REVERT: A 209 ASN cc_start: 0.8771 (t0) cc_final: 0.8341 (t0) REVERT: A 259 HIS cc_start: 0.8102 (p-80) cc_final: 0.7633 (p-80) REVERT: B 260 TRP cc_start: 0.8565 (t60) cc_final: 0.8279 (t60) REVERT: C 253 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7931 (ptp90) REVERT: D 173 ASN cc_start: 0.8788 (p0) cc_final: 0.8508 (p0) REVERT: D 174 MET cc_start: 0.7384 (ttt) cc_final: 0.7179 (ttt) REVERT: D 188 ASN cc_start: 0.8578 (t0) cc_final: 0.7370 (m-40) REVERT: E 98 ILE cc_start: 0.8998 (mt) cc_final: 0.8676 (mm) REVERT: E 188 ASN cc_start: 0.8212 (t0) cc_final: 0.7844 (t0) REVERT: E 197 MET cc_start: 0.8070 (ttp) cc_final: 0.7604 (ptm) REVERT: E 253 ARG cc_start: 0.8522 (mtm110) cc_final: 0.8055 (ptp-110) REVERT: E 259 HIS cc_start: 0.7604 (p90) cc_final: 0.7394 (p90) REVERT: F 64 GLN cc_start: 0.8056 (mt0) cc_final: 0.7793 (mm-40) REVERT: F 142 ILE cc_start: 0.8181 (mm) cc_final: 0.7799 (pt) REVERT: F 173 ASN cc_start: 0.8206 (p0) cc_final: 0.7954 (p0) REVERT: F 188 ASN cc_start: 0.8377 (t0) cc_final: 0.7457 (m-40) REVERT: F 260 TRP cc_start: 0.8491 (t60) cc_final: 0.8025 (t60) REVERT: G 185 ASP cc_start: 0.8135 (t0) cc_final: 0.7581 (t0) REVERT: G 188 ASN cc_start: 0.8612 (t0) cc_final: 0.8401 (t0) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.1532 time to fit residues: 78.2704 Evaluate side-chains 301 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 155 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 180 optimal weight: 0.2980 chunk 44 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN D 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.124213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.100742 restraints weight = 32906.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.102860 restraints weight = 24012.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.104424 restraints weight = 19386.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.105560 restraints weight = 16648.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.106195 restraints weight = 14964.274| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15890 Z= 0.177 Angle : 0.510 5.232 21511 Z= 0.283 Chirality : 0.044 0.135 2303 Planarity : 0.003 0.041 2758 Dihedral : 4.772 17.438 2079 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 31.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: -0.76 (0.19), residues: 1890 helix: None (None), residues: 0 sheet: 0.14 (0.17), residues: 924 loop : -1.13 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 253 TYR 0.019 0.002 TYR A 256 PHE 0.011 0.001 PHE F 224 TRP 0.016 0.001 TRP E 80 HIS 0.007 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (15890) covalent geometry : angle 0.51009 / 0.28 (21511) hydrogen bonds : bond 0.03519 / 2.25 ( 595) hydrogen bonds : angle 5.32711 / 3.64 ( 1926) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 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 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 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 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 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 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 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 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 327 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7877 (ttp80) REVERT: A 98 ILE cc_start: 0.8890 (mt) cc_final: 0.8675 (mt) REVERT: A 178 ASN cc_start: 0.9231 (m-40) cc_final: 0.8952 (m110) REVERT: A 209 ASN cc_start: 0.8592 (t0) cc_final: 0.8225 (t0) REVERT: A 259 HIS cc_start: 0.8109 (p-80) cc_final: 0.7603 (p-80) REVERT: B 260 TRP cc_start: 0.8538 (t60) cc_final: 0.8210 (t60) REVERT: C 253 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7986 (ptp90) REVERT: D 173 ASN cc_start: 0.8731 (p0) cc_final: 0.8483 (p0) REVERT: D 188 ASN cc_start: 0.8637 (t0) cc_final: 0.7381 (m-40) REVERT: D 256 TYR cc_start: 0.8393 (t80) cc_final: 0.7988 (t80) REVERT: E 98 ILE cc_start: 0.9027 (mt) cc_final: 0.8701 (mm) REVERT: E 188 ASN cc_start: 0.8208 (t0) cc_final: 0.7888 (t0) REVERT: E 197 MET cc_start: 0.7947 (ttp) cc_final: 0.7605 (ptm) REVERT: F 142 ILE cc_start: 0.8220 (mm) cc_final: 0.7875 (pt) REVERT: F 173 ASN cc_start: 0.8099 (p0) cc_final: 0.7858 (p0) REVERT: F 188 ASN cc_start: 0.8302 (t0) cc_final: 0.7328 (m-40) REVERT: F 260 TRP cc_start: 0.8488 (t60) cc_final: 0.8001 (t60) REVERT: G 185 ASP cc_start: 0.7885 (t0) cc_final: 0.7421 (t0) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1488 time to fit residues: 75.4243 Evaluate side-chains 298 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 124 optimal weight: 0.0060 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 194 GLN D 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.128096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.104117 restraints weight = 32588.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.106250 restraints weight = 23822.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.107969 restraints weight = 19152.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.108947 restraints weight = 16428.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.109474 restraints weight = 14826.481| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15890 Z= 0.124 Angle : 0.469 4.748 21511 Z= 0.262 Chirality : 0.043 0.135 2303 Planarity : 0.003 0.063 2758 Dihedral : 4.488 16.133 2079 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 30.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -0.73 (0.19), residues: 1890 helix: None (None), residues: 0 sheet: 0.03 (0.17), residues: 889 loop : -0.93 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 253 TYR 0.018 0.001 TYR A 256 PHE 0.010 0.001 PHE F 224 TRP 0.012 0.001 TRP E 80 HIS 0.006 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (15890) covalent geometry : angle 0.46878 / 0.26 (21511) hydrogen bonds : bond 0.03187 / 2.02 ( 595) hydrogen bonds : angle 5.10853 / 3.49 ( 1926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 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 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 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 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 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 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 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 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 337 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7851 (ttp80) REVERT: A 178 ASN cc_start: 0.9302 (m-40) cc_final: 0.8958 (m110) REVERT: A 209 ASN cc_start: 0.8582 (t0) cc_final: 0.8249 (t0) REVERT: B 204 MET cc_start: 0.7287 (ptm) cc_final: 0.6594 (ttp) REVERT: B 260 TRP cc_start: 0.8530 (t60) cc_final: 0.8201 (t60) REVERT: D 173 ASN cc_start: 0.8732 (p0) cc_final: 0.8479 (p0) REVERT: D 256 TYR cc_start: 0.8393 (t80) cc_final: 0.7978 (t80) REVERT: E 25 LEU cc_start: 0.9020 (mm) cc_final: 0.8407 (mt) REVERT: E 76 SER cc_start: 0.8934 (t) cc_final: 0.8684 (m) REVERT: E 98 ILE cc_start: 0.8972 (mt) cc_final: 0.8604 (mm) REVERT: E 188 ASN cc_start: 0.8104 (t0) cc_final: 0.7788 (t0) REVERT: E 197 MET cc_start: 0.7901 (ttp) cc_final: 0.7636 (ptm) REVERT: E 253 ARG cc_start: 0.8457 (mtm110) cc_final: 0.7993 (ptp-110) REVERT: F 142 ILE cc_start: 0.8205 (mm) cc_final: 0.7867 (pt) REVERT: F 173 ASN cc_start: 0.8086 (p0) cc_final: 0.7828 (p0) REVERT: F 188 ASN cc_start: 0.8283 (t0) cc_final: 0.7238 (m-40) REVERT: F 260 TRP cc_start: 0.8471 (t60) cc_final: 0.7981 (t60) REVERT: G 185 ASP cc_start: 0.7834 (t0) cc_final: 0.7367 (t0) REVERT: G 188 ASN cc_start: 0.8575 (t0) cc_final: 0.8350 (t0) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1509 time to fit residues: 78.9689 Evaluate side-chains 294 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 165 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 187 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.120893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.095879 restraints weight = 33222.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.098478 restraints weight = 23034.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.100283 restraints weight = 17911.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.101482 restraints weight = 15105.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.102276 restraints weight = 13420.295| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 15890 Z= 0.300 Angle : 0.629 10.454 21511 Z= 0.341 Chirality : 0.046 0.147 2303 Planarity : 0.004 0.062 2758 Dihedral : 5.230 18.915 2079 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 34.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -1.00 (0.19), residues: 1890 helix: None (None), residues: 0 sheet: -0.04 (0.18), residues: 875 loop : -1.23 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 251 TYR 0.022 0.002 TYR D 148 PHE 0.014 0.002 PHE D 224 TRP 0.024 0.001 TRP E 80 HIS 0.006 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.30 (15890) covalent geometry : angle 0.62871 / 0.34 (21511) hydrogen bonds : bond 0.04192 / 2.70 ( 595) hydrogen bonds : angle 5.56719 / 3.81 ( 1926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2949.85 seconds wall clock time: 52 minutes 5.37 seconds (3125.37 seconds total)