Starting phenix.real_space_refine on Fri Aug 7 07:14:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g0f_50932/08_2026/9g0f_50932_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g0f_50932/08_2026/9g0f_50932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g0f_50932/08_2026/9g0f_50932_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g0f_50932/08_2026/9g0f_50932_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g0f_50932/08_2026/9g0f_50932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g0f_50932/08_2026/9g0f_50932.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians P 52 5.49 5 Mg 7 5.21 5 S 56 5.16 5 C 12629 2.51 5 N 3526 2.21 5 O 3807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20077 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2672 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 13, 'TRANS': 317} Chain: "B" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "C" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "D" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "E" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "F" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "G" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "1" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.49, per 1000 atoms: 0.22 Number of scatterers: 20077 At special positions: 0 Unit cell: (96.2, 152.75, 155.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 52 15.00 Mg 7 11.99 O 3807 8.00 N 3526 7.00 C 12629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 960.4 milliseconds 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4516 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 10 sheets defined 64.3% alpha, 6.7% beta 16 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 62 through 85 Proline residue: A 80 - end of helix removed outlier: 4.182A pdb=" N SER A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.509A pdb=" N HIS A 124 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 172 through 178 removed outlier: 3.668A pdb=" N HIS A 175 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 200 removed outlier: 4.358A pdb=" N GLN A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.317A pdb=" N PHE A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.874A pdb=" N SER A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 255 Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 277 through 296 Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.581A pdb=" N ARG A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'B' and resid 8 through 14 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 62 through 83 Proline residue: B 80 - end of helix Processing helix chain 'B' and resid 105 through 117 removed outlier: 3.630A pdb=" N TYR B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 164 Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.619A pdb=" N HIS B 175 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 200 removed outlier: 3.931A pdb=" N ASP B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 215 removed outlier: 3.927A pdb=" N THR B 213 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 237 through 255 Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 266 through 273 Processing helix chain 'B' and resid 277 through 296 Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.546A pdb=" N ARG B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 332 through 344 Processing helix chain 'C' and resid 8 through 14 Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.864A pdb=" N GLU C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.560A pdb=" N GLU C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.226A pdb=" N LYS C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 164 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 183 through 200 removed outlier: 3.953A pdb=" N ASP C 187 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 215 Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 237 through 255 Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 266 through 273 Processing helix chain 'C' and resid 277 through 294 removed outlier: 3.567A pdb=" N LEU C 281 " --> pdb=" O CYS C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.740A pdb=" N ARG C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 329 removed outlier: 3.703A pdb=" N LYS C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 30 through 46 removed outlier: 3.611A pdb=" N GLU D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 79 Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 121 through 126 removed outlier: 4.062A pdb=" N LYS D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 121 through 126' Processing helix chain 'D' and resid 148 through 164 Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.645A pdb=" N HIS D 175 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 200 removed outlier: 3.727A pdb=" N LEU D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU D 192 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 237 through 255 Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 266 through 273 Processing helix chain 'D' and resid 277 through 295 removed outlier: 3.559A pdb=" N ASP D 294 " --> pdb=" O SER D 290 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.564A pdb=" N ARG D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 330 Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'E' and resid 8 through 14 Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 30 through 46 Processing helix chain 'E' and resid 62 through 79 Processing helix chain 'E' and resid 80 through 85 removed outlier: 4.873A pdb=" N GLU E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 148 through 164 Processing helix chain 'E' and resid 172 through 178 Processing helix chain 'E' and resid 183 through 200 removed outlier: 3.833A pdb=" N ASP E 187 " --> pdb=" O TYR E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 Processing helix chain 'E' and resid 218 through 224 Processing helix chain 'E' and resid 237 through 255 Processing helix chain 'E' and resid 263 through 265 No H-bonds generated for 'chain 'E' and resid 263 through 265' Processing helix chain 'E' and resid 266 through 275 Processing helix chain 'E' and resid 277 through 294 removed outlier: 3.682A pdb=" N LEU E 281 " --> pdb=" O CYS E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.743A pdb=" N ARG E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 329 Processing helix chain 'E' and resid 332 through 344 Processing helix chain 'F' and resid 8 through 14 Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 30 through 45 Processing helix chain 'F' and resid 62 through 79 removed outlier: 3.651A pdb=" N LEU F 68 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 85 removed outlier: 4.160A pdb=" N GLU F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.882A pdb=" N TYR F 109 " --> pdb=" O ASN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 125 Processing helix chain 'F' and resid 148 through 164 Processing helix chain 'F' and resid 172 through 178 removed outlier: 3.524A pdb=" N HIS F 175 " --> pdb=" O GLU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 200 removed outlier: 3.902A pdb=" N ASP F 187 " --> pdb=" O TYR F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 215 removed outlier: 3.959A pdb=" N THR F 213 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 224 Processing helix chain 'F' and resid 237 through 253 Processing helix chain 'F' and resid 266 through 273 Processing helix chain 'F' and resid 277 through 296 removed outlier: 3.544A pdb=" N LEU F 281 " --> pdb=" O CYS F 277 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG F 287 " --> pdb=" O ASP F 283 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 288 " --> pdb=" O TRP F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 308 removed outlier: 3.528A pdb=" N LYS F 307 " --> pdb=" O LYS F 303 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 327 Processing helix chain 'F' and resid 332 through 343 Processing helix chain 'G' and resid 8 through 14 Processing helix chain 'G' and resid 15 through 26 Processing helix chain 'G' and resid 30 through 46 Processing helix chain 'G' and resid 62 through 83 Proline residue: G 80 - end of helix Processing helix chain 'G' and resid 105 through 116 Processing helix chain 'G' and resid 121 through 125 removed outlier: 3.678A pdb=" N HIS G 124 " --> pdb=" O LEU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 164 Processing helix chain 'G' and resid 172 through 178 Processing helix chain 'G' and resid 184 through 200 Processing helix chain 'G' and resid 208 through 215 removed outlier: 3.758A pdb=" N LEU G 211 " --> pdb=" O THR G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 224 Processing helix chain 'G' and resid 237 through 255 Processing helix chain 'G' and resid 262 through 265 Processing helix chain 'G' and resid 266 through 273 Processing helix chain 'G' and resid 277 through 296 Processing helix chain 'G' and resid 301 through 308 removed outlier: 4.134A pdb=" N ARG G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 330 removed outlier: 3.514A pdb=" N LYS G 320 " --> pdb=" O GLN G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 344 removed outlier: 3.712A pdb=" N VAL G 336 " --> pdb=" O THR G 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 95 removed outlier: 6.721A pdb=" N VAL A 92 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP A 171 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 94 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 95 removed outlier: 3.644A pdb=" N VAL B 92 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE B 53 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLY B 207 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 55 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 56 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 95 removed outlier: 6.773A pdb=" N VAL C 92 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ASP C 171 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE C 94 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE C 168 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU C 206 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C 170 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY C 207 " --> pdb=" O VAL C 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AA5, first strand: chain 'D' and resid 91 through 95 removed outlier: 6.672A pdb=" N VAL D 92 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASP D 171 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 94 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE D 168 " --> pdb=" O CYS D 204 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU D 206 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL D 170 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE D 53 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY D 207 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL D 55 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE D 52 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE D 228 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHE D 54 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE D 230 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR D 56 " --> pdb=" O PHE D 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 134 through 135 Processing sheet with id=AA7, first strand: chain 'E' and resid 91 through 95 removed outlier: 6.638A pdb=" N VAL E 92 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASP E 171 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE E 94 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE E 168 " --> pdb=" O CYS E 204 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU E 206 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL E 170 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE E 53 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY E 207 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 55 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE E 52 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE E 228 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE E 54 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE E 230 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR E 56 " --> pdb=" O PHE E 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 133 through 135 Processing sheet with id=AA9, first strand: chain 'F' and resid 91 through 95 removed outlier: 6.722A pdb=" N VAL F 92 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASP F 171 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE F 94 " --> pdb=" O ASP F 171 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE F 168 " --> pdb=" O CYS F 204 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU F 206 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL F 170 " --> pdb=" O LEU F 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 92 through 94 removed outlier: 6.331A pdb=" N PHE G 168 " --> pdb=" O CYS G 204 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU G 206 " --> pdb=" O PHE G 168 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL G 170 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE G 53 " --> pdb=" O LEU G 205 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLY G 207 " --> pdb=" O ILE G 53 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL G 55 " --> pdb=" O GLY G 207 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 2895 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4103 1.33 - 1.45: 4886 1.45 - 1.57: 11403 1.57 - 1.69: 85 1.69 - 1.81: 77 Bond restraints: 20554 Sorted by residual: bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.541 0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.542 0.158 2.00e-02 2.50e+03 6.23e+01 bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.542 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" O3A ANP B 401 " pdb=" PB ANP B 401 " ideal model delta sigma weight residual 1.700 1.542 0.158 2.00e-02 2.50e+03 6.21e+01 bond pdb=" O3A ANP G 401 " pdb=" PB ANP G 401 " ideal model delta sigma weight residual 1.700 1.543 0.157 2.00e-02 2.50e+03 6.18e+01 ... (remaining 20549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 27842 4.85 - 9.71: 135 9.71 - 14.56: 17 14.56 - 19.41: 0 19.41 - 24.27: 7 Bond angle restraints: 28001 Sorted by residual: angle pdb=" N ASP C 136 " pdb=" CA ASP C 136 " pdb=" C ASP C 136 " ideal model delta sigma weight residual 113.18 100.72 12.46 1.21e+00 6.83e-01 1.06e+02 angle pdb=" N VAL F 61 " pdb=" CA VAL F 61 " pdb=" C VAL F 61 " ideal model delta sigma weight residual 110.72 119.87 -9.15 1.01e+00 9.80e-01 8.20e+01 angle pdb=" N LYS F 63 " pdb=" CA LYS F 63 " pdb=" C LYS F 63 " ideal model delta sigma weight residual 111.14 120.35 -9.21 1.08e+00 8.57e-01 7.26e+01 angle pdb=" N VAL E 61 " pdb=" CA VAL E 61 " pdb=" C VAL E 61 " ideal model delta sigma weight residual 110.72 119.26 -8.54 1.01e+00 9.80e-01 7.16e+01 angle pdb=" PB ANP G 401 " pdb=" N3B ANP G 401 " pdb=" PG ANP G 401 " ideal model delta sigma weight residual 126.95 102.68 24.27 3.00e+00 1.11e-01 6.54e+01 ... (remaining 27996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.16: 11293 24.16 - 48.31: 840 48.31 - 72.47: 201 72.47 - 96.63: 73 96.63 - 120.79: 7 Dihedral angle restraints: 12414 sinusoidal: 5425 harmonic: 6989 Sorted by residual: dihedral pdb=" C VAL E 61 " pdb=" N VAL E 61 " pdb=" CA VAL E 61 " pdb=" CB VAL E 61 " ideal model delta harmonic sigma weight residual -122.00 -133.86 11.86 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" CA PHE F 214 " pdb=" C PHE F 214 " pdb=" N ARG F 215 " pdb=" CA ARG F 215 " ideal model delta harmonic sigma weight residual -180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" C VAL F 61 " pdb=" N VAL F 61 " pdb=" CA VAL F 61 " pdb=" CB VAL F 61 " ideal model delta harmonic sigma weight residual -122.00 -132.45 10.45 0 2.50e+00 1.60e-01 1.75e+01 ... (remaining 12411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2974 0.105 - 0.211: 136 0.211 - 0.316: 17 0.316 - 0.422: 6 0.422 - 0.527: 3 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CA VAL F 61 " pdb=" N VAL F 61 " pdb=" C VAL F 61 " pdb=" CB VAL F 61 " both_signs ideal model delta sigma weight residual False 2.44 1.91 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CG LEU B 345 " pdb=" CB LEU B 345 " pdb=" CD1 LEU B 345 " pdb=" CD2 LEU B 345 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" CA LYS F 63 " pdb=" N LYS F 63 " pdb=" C LYS F 63 " pdb=" CB LYS F 63 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 3133 not shown) Planarity restraints: 3454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 21 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C ALA E 21 " -0.052 2.00e-02 2.50e+03 pdb=" O ALA E 21 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR E 22 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 57 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C GLY F 57 " 0.049 2.00e-02 2.50e+03 pdb=" O GLY F 57 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA F 58 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 135 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.29e+00 pdb=" C ARG C 135 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG C 135 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP C 136 " -0.015 2.00e-02 2.50e+03 ... (remaining 3451 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 134 2.50 - 3.10: 15170 3.10 - 3.70: 31960 3.70 - 4.30: 45154 4.30 - 4.90: 72904 Nonbonded interactions: 165322 Sorted by model distance: nonbonded pdb=" O1B ANP F 401 " pdb="MG MG F 402 " model vdw 1.900 2.170 nonbonded pdb=" O1B ANP C 401 " pdb="MG MG C 402 " model vdw 1.900 2.170 nonbonded pdb=" O1B ANP B 401 " pdb="MG MG B 402 " model vdw 1.900 2.170 nonbonded pdb=" O1B ANP G 401 " pdb="MG MG G 402 " model vdw 1.900 2.170 nonbonded pdb=" O1B ANP A 401 " pdb="MG MG A 402 " model vdw 1.901 2.170 ... (remaining 165317 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 '1' and resid 1 through 14) selection = (chain '2' and ((resid -14 and (name C4' or name O4' or name C3' or name O3' or \ name C2' or name C1' or name N9 or name C8 or name N7 or name C5 or name C6 or n \ ame N6 or name N1 or name C2 or name N3 or name C4 )) or resid -13 through -1)) } ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 5 through 335 or resid 401 through 402)) selection = (chain 'C' and (resid 5 through 335 or resid 401 through 402)) selection = (chain 'D' and (resid 5 through 335 or resid 401 through 402)) selection = (chain 'E' and (resid 5 through 335 or resid 401 through 402)) selection = (chain 'F' and (resid 5 through 335 or resid 401 through 402)) selection = (chain 'G' and (resid 5 through 335 or resid 401 through 402)) } 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: 12.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 21.360 Find NCS groups from input model: 0.560 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 0.007 0.159 20554 Z= 0.406 Angle : 0.968 24.267 28001 Z= 0.528 Chirality : 0.055 0.527 3136 Planarity : 0.004 0.051 3454 Dihedral : 18.558 120.785 7898 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 1.17 % Allowed : 12.69 % Favored : 86.14 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.18), residues: 2375 helix: 1.14 (0.14), residues: 1453 sheet: 0.54 (0.39), residues: 186 loop : -0.24 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 112 TYR 0.019 0.001 TYR D 37 PHE 0.015 0.001 PHE A 52 TRP 0.006 0.001 TRP G 284 HIS 0.006 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.41 (20554) covalent geometry : angle 0.96827 / 0.53 (28001) hydrogen bonds : bond 0.16626 / 11.17 ( 1096) hydrogen bonds : angle 5.64006 / 4.05 ( 2975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.9362 (mtm) cc_final: 0.8810 (mtm) REVERT: A 255 LEU cc_start: 0.9467 (pp) cc_final: 0.9240 (pt) REVERT: B 94 ILE cc_start: 0.9180 (tp) cc_final: 0.8901 (tt) REVERT: B 215 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8643 (ttt-90) REVERT: D 41 MET cc_start: 0.9342 (tpp) cc_final: 0.8906 (tpp) REVERT: D 46 GLU cc_start: 0.8678 (tp30) cc_final: 0.8211 (tp30) REVERT: E 59 SER cc_start: 0.7333 (OUTLIER) cc_final: 0.6812 (t) REVERT: E 61 VAL cc_start: 0.8713 (p) cc_final: 0.8479 (p) REVERT: E 63 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8623 (ptpp) REVERT: E 224 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7010 (mtt-85) REVERT: F 56 TYR cc_start: 0.7509 (p90) cc_final: 0.6900 (p90) REVERT: F 61 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.7922 (t) REVERT: F 63 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8345 (ptpp) REVERT: G 164 HIS cc_start: 0.7959 (t-170) cc_final: 0.7575 (t70) REVERT: G 175 HIS cc_start: 0.8956 (m-70) cc_final: 0.8603 (m-70) outliers start: 24 outliers final: 10 residues processed: 121 average time/residue: 0.1431 time to fit residues: 27.0730 Evaluate side-chains 89 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 135 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.0050 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS A 316 GLN B 124 HIS B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.067757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.046378 restraints weight = 84875.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.048190 restraints weight = 41509.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.049324 restraints weight = 26677.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.050046 restraints weight = 20453.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.050502 restraints weight = 17410.564| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 20554 Z= 0.162 Angle : 0.628 9.550 28001 Z= 0.320 Chirality : 0.043 0.249 3136 Planarity : 0.005 0.053 3454 Dihedral : 16.721 132.392 3254 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.94 % Allowed : 13.03 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.18), residues: 2375 helix: 1.06 (0.14), residues: 1492 sheet: 0.26 (0.38), residues: 196 loop : -0.10 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 153 TYR 0.017 0.001 TYR D 37 PHE 0.022 0.002 PHE B 126 TRP 0.020 0.001 TRP G 267 HIS 0.005 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (20554) covalent geometry : angle 0.62806 / 0.32 (28001) hydrogen bonds : bond 0.05005 / 3.28 ( 1096) hydrogen bonds : angle 4.29330 / 3.04 ( 2975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 85 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.9266 (mtm) cc_final: 0.8816 (mtm) REVERT: B 94 ILE cc_start: 0.9099 (tp) cc_final: 0.8807 (tt) REVERT: D 41 MET cc_start: 0.9340 (tpp) cc_final: 0.8767 (tpp) REVERT: D 46 GLU cc_start: 0.8734 (tp30) cc_final: 0.8171 (tp30) REVERT: D 187 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8495 (p0) REVERT: E 25 ASN cc_start: 0.9323 (m-40) cc_final: 0.8966 (m110) REVERT: E 224 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7381 (mtp85) REVERT: E 320 LYS cc_start: 0.9027 (tppt) cc_final: 0.8820 (tppt) REVERT: F 56 TYR cc_start: 0.7509 (p90) cc_final: 0.7078 (p90) REVERT: F 216 ASN cc_start: 0.8838 (m-40) cc_final: 0.8097 (t0) REVERT: G 164 HIS cc_start: 0.7934 (t-170) cc_final: 0.7617 (t70) REVERT: G 175 HIS cc_start: 0.9027 (m-70) cc_final: 0.8543 (m-70) outliers start: 40 outliers final: 20 residues processed: 118 average time/residue: 0.1171 time to fit residues: 22.9008 Evaluate side-chains 93 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 320 LYS Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 182 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 131 optimal weight: 0.0060 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.068207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.046642 restraints weight = 85366.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.048497 restraints weight = 40994.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.049671 restraints weight = 26184.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.050433 restraints weight = 19945.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.050903 restraints weight = 16915.985| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 : 0.002 0.055 20554 Z= 0.118 Angle : 0.560 11.874 28001 Z= 0.281 Chirality : 0.040 0.198 3136 Planarity : 0.004 0.046 3454 Dihedral : 15.562 128.701 3233 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.51 % Allowed : 13.90 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.99 (0.18), residues: 2375 helix: 1.17 (0.14), residues: 1484 sheet: 0.14 (0.38), residues: 197 loop : -0.11 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 215 TYR 0.017 0.001 TYR C 37 PHE 0.013 0.001 PHE A 251 TRP 0.008 0.001 TRP G 267 HIS 0.006 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (20554) covalent geometry : angle 0.55986 / 0.28 (28001) hydrogen bonds : bond 0.04352 / 2.87 ( 1096) hydrogen bonds : angle 4.00999 / 2.83 ( 2975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.9206 (mtm) cc_final: 0.8740 (mtm) REVERT: B 94 ILE cc_start: 0.9057 (tp) cc_final: 0.8765 (tt) REVERT: C 286 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.8971 (tptp) REVERT: D 41 MET cc_start: 0.9349 (tpp) cc_final: 0.8693 (tpp) REVERT: D 46 GLU cc_start: 0.8711 (tp30) cc_final: 0.8317 (tp30) REVERT: D 187 ASP cc_start: 0.9183 (OUTLIER) cc_final: 0.8491 (p0) REVERT: E 25 ASN cc_start: 0.9312 (m-40) cc_final: 0.8950 (m-40) REVERT: E 320 LYS cc_start: 0.9010 (tppt) cc_final: 0.8734 (tppt) REVERT: F 56 TYR cc_start: 0.7473 (p90) cc_final: 0.7008 (p90) REVERT: F 216 ASN cc_start: 0.8799 (m-40) cc_final: 0.8058 (t0) REVERT: G 164 HIS cc_start: 0.7946 (t-170) cc_final: 0.7579 (t-170) REVERT: G 175 HIS cc_start: 0.9032 (m-70) cc_final: 0.8527 (m-70) outliers start: 31 outliers final: 21 residues processed: 106 average time/residue: 0.1253 time to fit residues: 22.2295 Evaluate side-chains 93 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 107 optimal weight: 5.9990 chunk 152 optimal weight: 0.0010 chunk 21 optimal weight: 0.8980 chunk 83 optimal weight: 0.0470 chunk 136 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 208 optimal weight: 0.8980 chunk 169 optimal weight: 20.0000 overall best weight: 0.9686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.068264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.046575 restraints weight = 85236.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.048403 restraints weight = 41028.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.049587 restraints weight = 26367.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.050325 restraints weight = 20121.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.050767 restraints weight = 17126.602| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20554 Z= 0.110 Angle : 0.511 12.195 28001 Z= 0.260 Chirality : 0.039 0.159 3136 Planarity : 0.004 0.044 3454 Dihedral : 14.345 134.199 3229 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.94 % Allowed : 14.20 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.18), residues: 2375 helix: 1.27 (0.14), residues: 1485 sheet: 0.08 (0.38), residues: 196 loop : -0.12 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 215 TYR 0.016 0.001 TYR C 37 PHE 0.015 0.001 PHE D 168 TRP 0.005 0.001 TRP C 284 HIS 0.005 0.001 HIS E 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (20554) covalent geometry : angle 0.51123 / 0.26 (28001) hydrogen bonds : bond 0.03791 / 2.52 ( 1096) hydrogen bonds : angle 3.78506 / 2.66 ( 2975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 77 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 ILE cc_start: 0.9068 (tp) cc_final: 0.8788 (tt) REVERT: C 286 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9154 (tttt) REVERT: D 41 MET cc_start: 0.9369 (tpp) cc_final: 0.8855 (tpp) REVERT: D 46 GLU cc_start: 0.8733 (tp30) cc_final: 0.8334 (tp30) REVERT: D 187 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8492 (p0) REVERT: E 25 ASN cc_start: 0.9330 (m-40) cc_final: 0.8971 (m-40) REVERT: F 56 TYR cc_start: 0.7481 (p90) cc_final: 0.7111 (p90) REVERT: F 216 ASN cc_start: 0.8774 (m-40) cc_final: 0.7981 (t0) REVERT: G 164 HIS cc_start: 0.8045 (t-170) cc_final: 0.7628 (t-170) REVERT: G 175 HIS cc_start: 0.9057 (m-70) cc_final: 0.8554 (m-70) outliers start: 40 outliers final: 26 residues processed: 111 average time/residue: 0.1143 time to fit residues: 21.6285 Evaluate side-chains 98 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 90 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 229 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 214 optimal weight: 0.1980 chunk 164 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.066904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.045121 restraints weight = 85656.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.046890 restraints weight = 41606.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.048023 restraints weight = 26901.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.048729 restraints weight = 20648.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.049165 restraints weight = 17658.941| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20554 Z= 0.169 Angle : 0.552 11.920 28001 Z= 0.275 Chirality : 0.040 0.213 3136 Planarity : 0.004 0.043 3454 Dihedral : 14.073 134.759 3229 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.28 % Allowed : 14.29 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.18), residues: 2375 helix: 1.38 (0.14), residues: 1486 sheet: -0.07 (0.38), residues: 196 loop : -0.06 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 223 TYR 0.015 0.001 TYR C 37 PHE 0.013 0.001 PHE E 319 TRP 0.048 0.002 TRP G 267 HIS 0.003 0.001 HIS D 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (20554) covalent geometry : angle 0.55220 / 0.27 (28001) hydrogen bonds : bond 0.03839 / 2.57 ( 1096) hydrogen bonds : angle 3.81371 / 2.68 ( 2975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 71 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 ILE cc_start: 0.9127 (tp) cc_final: 0.8856 (tt) REVERT: C 286 LYS cc_start: 0.9453 (OUTLIER) cc_final: 0.8927 (tptp) REVERT: D 41 MET cc_start: 0.9399 (tpp) cc_final: 0.8853 (tpp) REVERT: D 46 GLU cc_start: 0.8797 (tp30) cc_final: 0.8419 (tp30) REVERT: D 187 ASP cc_start: 0.9207 (OUTLIER) cc_final: 0.8499 (p0) REVERT: E 25 ASN cc_start: 0.9355 (m-40) cc_final: 0.9043 (m110) REVERT: F 160 LEU cc_start: 0.9520 (tp) cc_final: 0.9284 (tp) REVERT: F 164 HIS cc_start: 0.8914 (t70) cc_final: 0.7997 (t70) REVERT: F 216 ASN cc_start: 0.8818 (m-40) cc_final: 0.8032 (t0) REVERT: G 164 HIS cc_start: 0.8215 (t-170) cc_final: 0.7777 (t-170) REVERT: G 175 HIS cc_start: 0.9119 (m-70) cc_final: 0.8628 (m-70) outliers start: 47 outliers final: 30 residues processed: 111 average time/residue: 0.1129 time to fit residues: 21.3114 Evaluate side-chains 100 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 206 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 199 optimal weight: 0.0770 chunk 17 optimal weight: 9.9990 chunk 223 optimal weight: 0.3980 chunk 150 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.067977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.046145 restraints weight = 84385.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.047952 restraints weight = 40971.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.049120 restraints weight = 26439.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049830 restraints weight = 20232.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.050290 restraints weight = 17268.236| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20554 Z= 0.097 Angle : 0.504 13.248 28001 Z= 0.252 Chirality : 0.039 0.171 3136 Planarity : 0.004 0.043 3454 Dihedral : 13.883 132.129 3229 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.85 % Allowed : 14.97 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.18), residues: 2375 helix: 1.39 (0.14), residues: 1486 sheet: -0.07 (0.38), residues: 196 loop : -0.04 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 135 TYR 0.016 0.001 TYR C 37 PHE 0.009 0.001 PHE A 52 TRP 0.038 0.001 TRP G 267 HIS 0.003 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (20554) covalent geometry : angle 0.50377 / 0.25 (28001) hydrogen bonds : bond 0.03584 / 2.39 ( 1096) hydrogen bonds : angle 3.67320 / 2.58 ( 2975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 76 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 ILE cc_start: 0.9097 (tp) cc_final: 0.8831 (tt) REVERT: C 286 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9153 (tttt) REVERT: D 41 MET cc_start: 0.9350 (tpp) cc_final: 0.8630 (tpp) REVERT: D 46 GLU cc_start: 0.8727 (tp30) cc_final: 0.8377 (tp30) REVERT: D 187 ASP cc_start: 0.9193 (OUTLIER) cc_final: 0.8470 (p0) REVERT: E 25 ASN cc_start: 0.9365 (m-40) cc_final: 0.9041 (m-40) REVERT: F 160 LEU cc_start: 0.9531 (tp) cc_final: 0.9296 (tp) REVERT: F 164 HIS cc_start: 0.8917 (t70) cc_final: 0.8034 (t70) REVERT: F 216 ASN cc_start: 0.8783 (m-40) cc_final: 0.7981 (t0) REVERT: G 164 HIS cc_start: 0.8221 (t-170) cc_final: 0.7775 (t-170) REVERT: G 175 HIS cc_start: 0.9133 (m-70) cc_final: 0.8652 (m-70) outliers start: 38 outliers final: 25 residues processed: 106 average time/residue: 0.1049 time to fit residues: 19.0797 Evaluate side-chains 96 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 28 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 171 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.066843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.044962 restraints weight = 85872.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.046658 restraints weight = 43279.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.047751 restraints weight = 28512.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.048434 restraints weight = 22181.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.048812 restraints weight = 19068.711| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20554 Z= 0.166 Angle : 0.541 13.068 28001 Z= 0.270 Chirality : 0.039 0.160 3136 Planarity : 0.004 0.042 3454 Dihedral : 13.844 133.721 3229 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.90 % Allowed : 14.97 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.18), residues: 2375 helix: 1.46 (0.14), residues: 1486 sheet: -0.17 (0.38), residues: 196 loop : -0.03 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 86 TYR 0.015 0.001 TYR A 109 PHE 0.011 0.001 PHE C 168 TRP 0.045 0.001 TRP G 267 HIS 0.004 0.001 HIS D 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (20554) covalent geometry : angle 0.54126 / 0.27 (28001) hydrogen bonds : bond 0.03704 / 2.49 ( 1096) hydrogen bonds : angle 3.72527 / 2.61 ( 2975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 71 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 ILE cc_start: 0.9022 (tp) cc_final: 0.8749 (tt) REVERT: C 286 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.8898 (tptp) REVERT: D 41 MET cc_start: 0.9362 (tpp) cc_final: 0.8696 (tpp) REVERT: D 46 GLU cc_start: 0.8833 (tp30) cc_final: 0.8449 (tp30) REVERT: D 187 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.8466 (p0) REVERT: E 25 ASN cc_start: 0.9407 (m-40) cc_final: 0.9071 (m-40) REVERT: F 160 LEU cc_start: 0.9530 (tp) cc_final: 0.9297 (tp) REVERT: F 164 HIS cc_start: 0.8967 (t70) cc_final: 0.8092 (t70) REVERT: F 216 ASN cc_start: 0.8860 (m-40) cc_final: 0.8033 (t0) REVERT: G 164 HIS cc_start: 0.8251 (t-170) cc_final: 0.7742 (t-170) REVERT: G 175 HIS cc_start: 0.9154 (m-70) cc_final: 0.8697 (m-70) outliers start: 39 outliers final: 28 residues processed: 103 average time/residue: 0.1098 time to fit residues: 19.5085 Evaluate side-chains 98 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.067508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.045652 restraints weight = 85186.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.047376 restraints weight = 42689.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.048481 restraints weight = 28044.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.049182 restraints weight = 21728.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.049609 restraints weight = 18645.563| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20554 Z= 0.113 Angle : 0.508 14.239 28001 Z= 0.255 Chirality : 0.039 0.177 3136 Planarity : 0.004 0.042 3454 Dihedral : 13.715 131.036 3229 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.80 % Allowed : 15.31 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.18), residues: 2375 helix: 1.46 (0.14), residues: 1486 sheet: -0.13 (0.38), residues: 196 loop : -0.02 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 86 TYR 0.017 0.001 TYR C 37 PHE 0.008 0.001 PHE A 52 TRP 0.048 0.001 TRP G 267 HIS 0.004 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (20554) covalent geometry : angle 0.50751 / 0.26 (28001) hydrogen bonds : bond 0.03540 / 2.37 ( 1096) hydrogen bonds : angle 3.63608 / 2.55 ( 2975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9557 (t0) cc_final: 0.9113 (t0) REVERT: B 94 ILE cc_start: 0.9017 (tp) cc_final: 0.8741 (tt) REVERT: C 286 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9173 (tttt) REVERT: D 41 MET cc_start: 0.9324 (tpp) cc_final: 0.8578 (tpp) REVERT: D 46 GLU cc_start: 0.8779 (tp30) cc_final: 0.8362 (tp30) REVERT: D 187 ASP cc_start: 0.9230 (OUTLIER) cc_final: 0.8472 (p0) REVERT: E 25 ASN cc_start: 0.9398 (m-40) cc_final: 0.9071 (m-40) REVERT: E 198 MET cc_start: 0.9040 (ttp) cc_final: 0.8818 (ttp) REVERT: F 69 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8642 (tmm-80) REVERT: F 160 LEU cc_start: 0.9547 (tp) cc_final: 0.9318 (tp) REVERT: F 164 HIS cc_start: 0.8942 (t70) cc_final: 0.8141 (t70) REVERT: F 216 ASN cc_start: 0.8842 (m-40) cc_final: 0.7990 (t0) REVERT: G 164 HIS cc_start: 0.8298 (t-170) cc_final: 0.7792 (t-170) REVERT: G 175 HIS cc_start: 0.9185 (m-70) cc_final: 0.8731 (m-70) outliers start: 37 outliers final: 27 residues processed: 108 average time/residue: 0.1134 time to fit residues: 20.6763 Evaluate side-chains 100 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 94 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 228 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.066603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.044719 restraints weight = 85644.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.046407 restraints weight = 43292.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.047477 restraints weight = 28589.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.048160 restraints weight = 22254.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.048577 restraints weight = 19166.897| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20554 Z= 0.161 Angle : 0.552 14.050 28001 Z= 0.273 Chirality : 0.040 0.191 3136 Planarity : 0.004 0.041 3454 Dihedral : 13.682 130.965 3229 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.85 % Allowed : 15.41 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.18), residues: 2375 helix: 1.47 (0.14), residues: 1486 sheet: -0.22 (0.38), residues: 196 loop : -0.01 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 14 TYR 0.013 0.001 TYR C 37 PHE 0.011 0.001 PHE C 168 TRP 0.048 0.001 TRP G 267 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (20554) covalent geometry : angle 0.55157 / 0.27 (28001) hydrogen bonds : bond 0.03661 / 2.46 ( 1096) hydrogen bonds : angle 3.71527 / 2.59 ( 2975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 69 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9545 (t0) cc_final: 0.9113 (t0) REVERT: B 94 ILE cc_start: 0.9013 (tp) cc_final: 0.8744 (tt) REVERT: D 41 MET cc_start: 0.9331 (tpp) cc_final: 0.8674 (tpp) REVERT: D 187 ASP cc_start: 0.9256 (OUTLIER) cc_final: 0.8474 (p0) REVERT: E 25 ASN cc_start: 0.9427 (m-40) cc_final: 0.9103 (m-40) REVERT: E 198 MET cc_start: 0.9036 (ttp) cc_final: 0.8828 (ttp) REVERT: F 160 LEU cc_start: 0.9559 (tp) cc_final: 0.9334 (tp) REVERT: F 164 HIS cc_start: 0.8964 (t70) cc_final: 0.8196 (t70) REVERT: F 216 ASN cc_start: 0.8916 (m-40) cc_final: 0.8088 (t0) REVERT: G 164 HIS cc_start: 0.8387 (t-170) cc_final: 0.7883 (t70) REVERT: G 175 HIS cc_start: 0.9208 (m-70) cc_final: 0.8656 (m-70) outliers start: 38 outliers final: 29 residues processed: 104 average time/residue: 0.1058 time to fit residues: 19.1119 Evaluate side-chains 96 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 186 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.066276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.044364 restraints weight = 86064.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.046031 restraints weight = 43581.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.047112 restraints weight = 28793.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.047774 restraints weight = 22386.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048202 restraints weight = 19287.797| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20554 Z= 0.185 Angle : 0.562 14.009 28001 Z= 0.281 Chirality : 0.040 0.181 3136 Planarity : 0.004 0.042 3454 Dihedral : 13.668 129.924 3229 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.75 % Allowed : 15.56 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.25 (0.18), residues: 2375 helix: 1.44 (0.14), residues: 1486 sheet: -0.26 (0.37), residues: 196 loop : -0.02 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 224 TYR 0.015 0.001 TYR F 56 PHE 0.013 0.001 PHE C 168 TRP 0.053 0.002 TRP G 267 HIS 0.005 0.001 HIS E 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (20554) covalent geometry : angle 0.56220 / 0.28 (28001) hydrogen bonds : bond 0.03721 / 2.51 ( 1096) hydrogen bonds : angle 3.75856 / 2.62 ( 2975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 67 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9547 (t0) cc_final: 0.9113 (t0) REVERT: B 94 ILE cc_start: 0.9015 (tp) cc_final: 0.8747 (tt) REVERT: D 41 MET cc_start: 0.9339 (tpp) cc_final: 0.8684 (tpp) REVERT: D 187 ASP cc_start: 0.9260 (OUTLIER) cc_final: 0.8485 (p0) REVERT: E 25 ASN cc_start: 0.9426 (m-40) cc_final: 0.9101 (m-40) REVERT: F 69 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8642 (tmm-80) REVERT: F 160 LEU cc_start: 0.9568 (tp) cc_final: 0.9345 (tp) REVERT: F 164 HIS cc_start: 0.8972 (t70) cc_final: 0.8256 (t-90) REVERT: G 164 HIS cc_start: 0.8400 (t-170) cc_final: 0.7899 (t70) REVERT: G 175 HIS cc_start: 0.9211 (m-70) cc_final: 0.8663 (m-70) outliers start: 36 outliers final: 29 residues processed: 100 average time/residue: 0.1111 time to fit residues: 19.0564 Evaluate side-chains 97 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 146 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 238 optimal weight: 40.0000 chunk 38 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.065274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.043482 restraints weight = 86661.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.044933 restraints weight = 48343.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.045853 restraints weight = 33830.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.046438 restraints weight = 27324.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.046778 restraints weight = 24061.946| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 20554 Z= 0.276 Angle : 0.686 13.295 28001 Z= 0.336 Chirality : 0.042 0.192 3136 Planarity : 0.005 0.041 3454 Dihedral : 13.817 131.255 3229 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.56 % Allowed : 15.85 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.18), residues: 2375 helix: 1.28 (0.14), residues: 1481 sheet: -0.51 (0.36), residues: 196 loop : -0.12 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 14 TYR 0.019 0.002 TYR D 209 PHE 0.018 0.002 PHE F 168 TRP 0.052 0.002 TRP G 267 HIS 0.006 0.001 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.28 (20554) covalent geometry : angle 0.68589 / 0.34 (28001) hydrogen bonds : bond 0.04267 / 2.90 ( 1096) hydrogen bonds : angle 4.06691 / 2.84 ( 2975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3099.94 seconds wall clock time: 54 minutes 35.48 seconds (3275.48 seconds total)