Starting phenix.real_space_refine on Tue Jun 17 18:12:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g0f_50932/06_2025/9g0f_50932_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g0f_50932/06_2025/9g0f_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9g0f_50932/06_2025/9g0f_50932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g0f_50932/06_2025/9g0f_50932.map" model { file = "/net/cci-nas-00/data/ceres_data/9g0f_50932/06_2025/9g0f_50932_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g0f_50932/06_2025/9g0f_50932_neut.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.32, per 1000 atoms: 0.66 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: 4.69 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 6.18 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: 6.56 Time building geometry restraints manager: 5.61 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: 27841 4.85 - 9.71: 136 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: 2975 0.105 - 0.211: 135 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: 10.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 49.270 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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= 0.400 Angle : 0.972 24.267 28001 Z= 0.525 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 : 9.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP G 284 HIS 0.006 0.001 HIS A 175 PHE 0.015 0.001 PHE A 52 TYR 0.019 0.001 TYR D 37 ARG 0.005 0.000 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.16626 ( 1096) hydrogen bonds : angle 5.64006 ( 2975) covalent geometry : bond 0.00681 (20554) covalent geometry : angle 0.97199 (28001) *********************** 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 : 2.419 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: 0.9241 (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: 0.3471 time to fit residues: 65.0853 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 : 2.156 ------------------------------------------------------------------------------- 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 201 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 96 optimal weight: 0.0370 chunk 187 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 217 optimal weight: 0.7980 overall best weight: 1.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN B 124 HIS B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.067788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.046282 restraints weight = 85146.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.048091 restraints weight = 41152.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049262 restraints weight = 26438.741| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20554 Z= 0.143 Angle : 0.574 11.956 28001 Z= 0.292 Chirality : 0.040 0.145 3136 Planarity : 0.004 0.050 3454 Dihedral : 15.811 132.060 3254 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.99 % Allowed : 13.22 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.18), residues: 2375 helix: 1.17 (0.14), residues: 1485 sheet: 0.22 (0.38), residues: 196 loop : -0.07 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 267 HIS 0.004 0.001 HIS C 164 PHE 0.023 0.001 PHE B 126 TYR 0.016 0.001 TYR C 37 ARG 0.005 0.000 ARG A 215 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 1096) hydrogen bonds : angle 4.09165 ( 2975) covalent geometry : bond 0.00310 (20554) covalent geometry : angle 0.57354 (28001) *********************** 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 133 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.9184 (mtm) cc_final: 0.8785 (mtm) REVERT: B 94 ILE cc_start: 0.9103 (tp) cc_final: 0.8812 (tt) REVERT: B 263 LEU cc_start: 0.9624 (mt) cc_final: 0.9421 (mp) REVERT: D 41 MET cc_start: 0.9336 (tpp) cc_final: 0.8749 (tpp) REVERT: D 46 GLU cc_start: 0.8741 (tp30) cc_final: 0.8160 (tp30) REVERT: E 25 ASN cc_start: 0.9303 (m-40) cc_final: 0.8965 (m110) REVERT: F 56 TYR cc_start: 0.7547 (p90) cc_final: 0.7143 (p90) REVERT: F 216 ASN cc_start: 0.8850 (m-40) cc_final: 0.8175 (t0) REVERT: G 164 HIS cc_start: 0.7949 (t-170) cc_final: 0.7569 (t-170) REVERT: G 175 HIS cc_start: 0.9012 (m-70) cc_final: 0.8531 (m-70) outliers start: 41 outliers final: 24 residues processed: 126 average time/residue: 0.4348 time to fit residues: 97.0202 Evaluate side-chains 96 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 3.287 ------------------------------------------------------------------------------- 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 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 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 299 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR 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 81 optimal weight: 0.9990 chunk 169 optimal weight: 20.0000 chunk 125 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 50 optimal weight: 0.0870 chunk 168 optimal weight: 6.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS C 254 HIS G 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.068613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.046996 restraints weight = 84359.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.048843 restraints weight = 40648.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.050037 restraints weight = 26071.268| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20554 Z= 0.104 Angle : 0.502 11.187 28001 Z= 0.255 Chirality : 0.039 0.158 3136 Planarity : 0.004 0.045 3454 Dihedral : 13.975 134.475 3229 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.04 % Allowed : 13.66 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2375 helix: 1.28 (0.14), residues: 1486 sheet: 0.14 (0.39), residues: 196 loop : -0.01 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP G 267 HIS 0.003 0.001 HIS D 30 PHE 0.010 0.001 PHE A 52 TYR 0.015 0.001 TYR A 109 ARG 0.003 0.000 ARG F 112 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 1096) hydrogen bonds : angle 3.76374 ( 2975) covalent geometry : bond 0.00223 (20554) covalent geometry : angle 0.50222 (28001) *********************** 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 129 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 87 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 ILE cc_start: 0.9128 (tp) cc_final: 0.8860 (tt) REVERT: C 286 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9161 (tttt) REVERT: D 41 MET cc_start: 0.9365 (tpp) cc_final: 0.8895 (tpp) REVERT: D 46 GLU cc_start: 0.8700 (tp30) cc_final: 0.8382 (tp30) REVERT: D 187 ASP cc_start: 0.9210 (OUTLIER) cc_final: 0.8526 (p0) REVERT: E 25 ASN cc_start: 0.9325 (m-40) cc_final: 0.8998 (m110) REVERT: F 56 TYR cc_start: 0.7472 (p90) cc_final: 0.7024 (p90) REVERT: F 69 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8558 (tmm-80) REVERT: F 160 LEU cc_start: 0.9618 (tp) cc_final: 0.9369 (tp) REVERT: F 164 HIS cc_start: 0.8913 (t70) cc_final: 0.8085 (t70) REVERT: F 216 ASN cc_start: 0.8793 (m-40) cc_final: 0.8031 (t0) REVERT: G 164 HIS cc_start: 0.8104 (t-170) cc_final: 0.7657 (t-170) REVERT: G 175 HIS cc_start: 0.9056 (m-70) cc_final: 0.8557 (m-70) outliers start: 42 outliers final: 22 residues processed: 122 average time/residue: 0.4432 time to fit residues: 87.9756 Evaluate side-chains 97 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 4.334 ------------------------------------------------------------------------------- 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 19 ARG 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 E residue 28 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 69 ARG 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 71 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 232 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 51 optimal weight: 8.9990 chunk 23 optimal weight: 0.4980 chunk 131 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3494 r_free = 0.3494 target = 0.067612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045775 restraints weight = 85449.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.047566 restraints weight = 41509.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.048714 restraints weight = 26860.769| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20554 Z= 0.130 Angle : 0.507 12.138 28001 Z= 0.255 Chirality : 0.038 0.140 3136 Planarity : 0.004 0.043 3454 Dihedral : 13.711 134.669 3227 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.19 % Allowed : 14.34 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 2375 helix: 1.42 (0.14), residues: 1486 sheet: -0.01 (0.38), residues: 196 loop : 0.01 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP G 267 HIS 0.004 0.001 HIS D 30 PHE 0.013 0.001 PHE D 168 TYR 0.014 0.001 TYR C 37 ARG 0.003 0.000 ARG E 215 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 1096) hydrogen bonds : angle 3.70992 ( 2975) covalent geometry : bond 0.00289 (20554) covalent geometry : angle 0.50717 (28001) *********************** 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 118 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 73 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.9004 (mtm) cc_final: 0.8626 (mtm) REVERT: B 94 ILE cc_start: 0.9133 (tp) cc_final: 0.8875 (tt) REVERT: C 286 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.8945 (tptp) REVERT: D 41 MET cc_start: 0.9371 (tpp) cc_final: 0.8887 (tpp) REVERT: D 46 GLU cc_start: 0.8771 (tp30) cc_final: 0.8377 (tp30) REVERT: D 187 ASP cc_start: 0.9231 (OUTLIER) cc_final: 0.8509 (p0) REVERT: E 25 ASN cc_start: 0.9363 (m-40) cc_final: 0.9041 (m110) REVERT: F 69 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8664 (tmm-80) REVERT: F 160 LEU cc_start: 0.9620 (tp) cc_final: 0.9382 (tp) REVERT: F 164 HIS cc_start: 0.8922 (t70) cc_final: 0.8168 (t70) REVERT: F 216 ASN cc_start: 0.8801 (m-40) cc_final: 0.8014 (t0) REVERT: G 164 HIS cc_start: 0.8227 (t-170) cc_final: 0.7708 (t70) REVERT: G 175 HIS cc_start: 0.9135 (m-70) cc_final: 0.8648 (m-70) outliers start: 45 outliers final: 25 residues processed: 110 average time/residue: 0.2895 time to fit residues: 52.8828 Evaluate side-chains 97 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 2.256 ------------------------------------------------------------------------------- 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 19 ARG 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 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 E residue 318 MET Chi-restraints excluded: chain F residue 69 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 231 optimal weight: 30.0000 chunk 13 optimal weight: 30.0000 chunk 129 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 213 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 225 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 171 optimal weight: 0.3980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.067625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.045885 restraints weight = 84942.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.047671 restraints weight = 41137.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.048797 restraints weight = 26567.394| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20554 Z= 0.116 Angle : 0.502 12.943 28001 Z= 0.251 Chirality : 0.038 0.225 3136 Planarity : 0.004 0.042 3454 Dihedral : 13.575 132.543 3227 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.85 % Allowed : 14.92 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.18), residues: 2375 helix: 1.47 (0.14), residues: 1486 sheet: -0.12 (0.38), residues: 196 loop : 0.03 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP G 267 HIS 0.003 0.001 HIS D 30 PHE 0.011 0.001 PHE A 52 TYR 0.012 0.001 TYR C 37 ARG 0.015 0.000 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 1096) hydrogen bonds : angle 3.63240 ( 2975) covalent geometry : bond 0.00256 (20554) covalent geometry : angle 0.50233 (28001) *********************** 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 114 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 76 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9569 (t0) cc_final: 0.9122 (t0) REVERT: A 198 MET cc_start: 0.8892 (mtm) cc_final: 0.8490 (mtm) REVERT: B 56 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.8375 (p90) REVERT: B 94 ILE cc_start: 0.9119 (tp) cc_final: 0.8867 (tt) REVERT: C 286 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9180 (tttt) REVERT: D 41 MET cc_start: 0.9328 (tpp) cc_final: 0.8613 (tpp) REVERT: D 46 GLU cc_start: 0.8748 (tp30) cc_final: 0.8406 (tp30) REVERT: D 187 ASP cc_start: 0.9224 (OUTLIER) cc_final: 0.8496 (p0) REVERT: E 25 ASN cc_start: 0.9375 (m-40) cc_final: 0.9052 (m110) REVERT: F 69 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8668 (tmm-80) REVERT: F 160 LEU cc_start: 0.9627 (tp) cc_final: 0.9403 (tp) REVERT: F 164 HIS cc_start: 0.8934 (t70) cc_final: 0.8233 (t70) REVERT: F 216 ASN cc_start: 0.8813 (m-40) cc_final: 0.8012 (t0) REVERT: G 164 HIS cc_start: 0.8349 (t-170) cc_final: 0.7837 (t70) REVERT: G 175 HIS cc_start: 0.9186 (m-70) cc_final: 0.8724 (m-70) outliers start: 38 outliers final: 28 residues processed: 108 average time/residue: 0.2848 time to fit residues: 51.6258 Evaluate side-chains 103 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 2.403 ------------------------------------------------------------------------------- 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 19 ARG Chi-restraints excluded: chain B residue 56 TYR 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 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 205 LEU 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 54 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 56 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.067688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.045602 restraints weight = 85126.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.047213 restraints weight = 45734.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.048215 restraints weight = 31223.575| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20554 Z= 0.123 Angle : 0.500 13.287 28001 Z= 0.249 Chirality : 0.038 0.195 3136 Planarity : 0.004 0.041 3454 Dihedral : 13.485 128.849 3227 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.19 % Allowed : 14.58 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.18), residues: 2375 helix: 1.57 (0.14), residues: 1480 sheet: -0.21 (0.37), residues: 196 loop : 0.16 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP G 267 HIS 0.003 0.001 HIS D 254 PHE 0.011 0.001 PHE A 52 TYR 0.012 0.001 TYR C 37 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 1096) hydrogen bonds : angle 3.59652 ( 2975) covalent geometry : bond 0.00272 (20554) covalent geometry : angle 0.50006 (28001) *********************** 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 123 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 78 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9563 (t0) cc_final: 0.9140 (t0) REVERT: A 198 MET cc_start: 0.8826 (mtm) cc_final: 0.8456 (mtm) REVERT: B 56 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8185 (p90) REVERT: B 94 ILE cc_start: 0.9314 (tp) cc_final: 0.9090 (tt) REVERT: C 286 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9170 (tttt) REVERT: D 41 MET cc_start: 0.9243 (tpp) cc_final: 0.8748 (tpp) REVERT: D 46 GLU cc_start: 0.8603 (tp30) cc_final: 0.8398 (tp30) REVERT: D 187 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8443 (p0) REVERT: D 335 ASP cc_start: 0.8951 (m-30) cc_final: 0.8723 (m-30) REVERT: E 25 ASN cc_start: 0.9241 (m-40) cc_final: 0.8969 (m110) REVERT: F 69 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8755 (tmm-80) REVERT: F 164 HIS cc_start: 0.8710 (t70) cc_final: 0.8459 (t70) REVERT: F 216 ASN cc_start: 0.8603 (m-40) cc_final: 0.7806 (t0) REVERT: G 164 HIS cc_start: 0.8497 (t-170) cc_final: 0.7993 (t70) REVERT: G 175 HIS cc_start: 0.9273 (m-70) cc_final: 0.8812 (m-70) outliers start: 45 outliers final: 25 residues processed: 116 average time/residue: 0.2759 time to fit residues: 53.0654 Evaluate side-chains 102 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 56 TYR 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 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 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 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 66 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 229 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.066760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.044813 restraints weight = 85693.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.046385 restraints weight = 45703.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.047386 restraints weight = 31186.178| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2365 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= 0.184 Angle : 0.556 13.481 28001 Z= 0.278 Chirality : 0.040 0.243 3136 Planarity : 0.004 0.041 3454 Dihedral : 13.554 127.707 3227 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.04 % Allowed : 14.97 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.18), residues: 2375 helix: 1.56 (0.14), residues: 1480 sheet: -0.37 (0.37), residues: 196 loop : 0.15 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP G 267 HIS 0.004 0.001 HIS D 254 PHE 0.013 0.001 PHE D 168 TYR 0.015 0.001 TYR F 56 ARG 0.003 0.000 ARG B 273 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 1096) hydrogen bonds : angle 3.73626 ( 2975) covalent geometry : bond 0.00411 (20554) covalent geometry : angle 0.55567 (28001) *********************** 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 112 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 70 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9568 (t0) cc_final: 0.9150 (t0) REVERT: A 198 MET cc_start: 0.8788 (mtm) cc_final: 0.8405 (mtm) REVERT: B 56 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.8270 (p90) REVERT: B 94 ILE cc_start: 0.9325 (tp) cc_final: 0.9108 (tt) REVERT: C 286 LYS cc_start: 0.9525 (OUTLIER) cc_final: 0.8945 (tptp) REVERT: D 41 MET cc_start: 0.9306 (tpp) cc_final: 0.8864 (tpp) REVERT: D 187 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8430 (p0) REVERT: E 25 ASN cc_start: 0.9287 (m-40) cc_final: 0.9019 (m110) REVERT: F 69 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8718 (tmm-80) REVERT: F 164 HIS cc_start: 0.8792 (t70) cc_final: 0.8495 (t70) REVERT: G 164 HIS cc_start: 0.8548 (t-170) cc_final: 0.8054 (t70) REVERT: G 175 HIS cc_start: 0.9288 (m-70) cc_final: 0.8740 (m-70) outliers start: 42 outliers final: 28 residues processed: 108 average time/residue: 0.2853 time to fit residues: 52.1750 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 : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 56 TYR 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 72 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 chunk 189 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 chunk 71 optimal weight: 0.0050 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.068823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.047039 restraints weight = 85004.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.048705 restraints weight = 44751.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049764 restraints weight = 30183.368| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20554 Z= 0.095 Angle : 0.503 14.690 28001 Z= 0.248 Chirality : 0.038 0.181 3136 Planarity : 0.003 0.040 3454 Dihedral : 13.433 123.642 3227 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.56 % Allowed : 15.65 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2375 helix: 1.54 (0.14), residues: 1480 sheet: -0.28 (0.37), residues: 196 loop : 0.20 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP G 267 HIS 0.003 0.001 HIS B 30 PHE 0.009 0.001 PHE C 54 TYR 0.013 0.001 TYR C 37 ARG 0.003 0.000 ARG E 223 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 1096) hydrogen bonds : angle 3.51497 ( 2975) covalent geometry : bond 0.00203 (20554) covalent geometry : angle 0.50306 (28001) *********************** 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 120 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9571 (t0) cc_final: 0.9163 (t0) REVERT: A 198 MET cc_start: 0.8810 (mtm) cc_final: 0.8449 (mtm) REVERT: B 56 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.8191 (p90) REVERT: B 94 ILE cc_start: 0.9274 (tp) cc_final: 0.9042 (tt) REVERT: D 41 MET cc_start: 0.9176 (tpp) cc_final: 0.8741 (tpp) REVERT: D 46 GLU cc_start: 0.8507 (tp30) cc_final: 0.8241 (tp30) REVERT: D 187 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8426 (p0) REVERT: D 335 ASP cc_start: 0.8925 (m-30) cc_final: 0.8699 (m-30) REVERT: E 25 ASN cc_start: 0.9268 (m-40) cc_final: 0.8990 (m110) REVERT: F 69 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8722 (tmm-80) REVERT: F 216 ASN cc_start: 0.8631 (m-40) cc_final: 0.7979 (t0) REVERT: G 164 HIS cc_start: 0.8557 (t-170) cc_final: 0.8066 (t70) REVERT: G 175 HIS cc_start: 0.9322 (m-70) cc_final: 0.8868 (m-70) REVERT: G 267 TRP cc_start: 0.9318 (p-90) cc_final: 0.8936 (p-90) outliers start: 32 outliers final: 22 residues processed: 115 average time/residue: 0.2644 time to fit residues: 51.2224 Evaluate side-chains 102 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 2.256 ------------------------------------------------------------------------------- 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 56 TYR 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 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 252 GLN 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 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 38 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 161 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 160 optimal weight: 0.2980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.067699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.045788 restraints weight = 85344.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.047398 restraints weight = 45576.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048415 restraints weight = 30991.196| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20554 Z= 0.148 Angle : 0.527 13.693 28001 Z= 0.263 Chirality : 0.039 0.176 3136 Planarity : 0.004 0.039 3454 Dihedral : 13.384 124.397 3226 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.60 % Allowed : 16.14 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2375 helix: 1.60 (0.14), residues: 1480 sheet: -0.31 (0.37), residues: 196 loop : 0.22 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP G 267 HIS 0.021 0.001 HIS F 164 PHE 0.010 0.001 PHE C 168 TYR 0.016 0.001 TYR A 109 ARG 0.002 0.000 ARG B 14 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 1096) hydrogen bonds : angle 3.58194 ( 2975) covalent geometry : bond 0.00327 (20554) covalent geometry : angle 0.52723 (28001) *********************** 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 111 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9581 (t0) cc_final: 0.9163 (t0) REVERT: A 198 MET cc_start: 0.8786 (mtm) cc_final: 0.8409 (mtm) REVERT: B 56 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8230 (p90) REVERT: B 94 ILE cc_start: 0.9316 (tp) cc_final: 0.9092 (tt) REVERT: B 137 ASN cc_start: 0.8500 (t0) cc_final: 0.8232 (t0) REVERT: D 41 MET cc_start: 0.9256 (tpp) cc_final: 0.8888 (tpp) REVERT: D 187 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8448 (p0) REVERT: D 335 ASP cc_start: 0.8927 (m-30) cc_final: 0.8699 (m-30) REVERT: E 25 ASN cc_start: 0.9292 (m-40) cc_final: 0.9019 (m110) REVERT: F 69 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8750 (tmm-80) REVERT: G 164 HIS cc_start: 0.8598 (t-170) cc_final: 0.8133 (t70) REVERT: G 175 HIS cc_start: 0.9220 (m-70) cc_final: 0.8787 (m-70) REVERT: G 230 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7902 (t80) outliers start: 33 outliers final: 23 residues processed: 109 average time/residue: 0.2857 time to fit residues: 52.4471 Evaluate side-chains 101 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 2.164 ------------------------------------------------------------------------------- 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 56 TYR 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 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR 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 230 PHE 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 156 optimal weight: 0.0000 chunk 185 optimal weight: 0.4980 chunk 220 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 71 optimal weight: 0.0970 chunk 10 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 231 optimal weight: 8.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.068769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.047044 restraints weight = 85172.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.048699 restraints weight = 44863.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049773 restraints weight = 30322.277| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20554 Z= 0.096 Angle : 0.497 13.827 28001 Z= 0.247 Chirality : 0.038 0.140 3136 Planarity : 0.004 0.040 3454 Dihedral : 13.269 121.751 3226 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.31 % Allowed : 16.77 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2375 helix: 1.58 (0.14), residues: 1480 sheet: -0.26 (0.38), residues: 196 loop : 0.24 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP G 267 HIS 0.024 0.001 HIS F 164 PHE 0.009 0.001 PHE C 23 TYR 0.015 0.001 TYR A 109 ARG 0.003 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 1096) hydrogen bonds : angle 3.46714 ( 2975) covalent geometry : bond 0.00206 (20554) covalent geometry : angle 0.49683 (28001) ********************** 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 109 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9577 (t0) cc_final: 0.9157 (t0) REVERT: A 198 MET cc_start: 0.8830 (mtm) cc_final: 0.8451 (mtm) REVERT: B 56 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8182 (p90) REVERT: B 94 ILE cc_start: 0.9276 (tp) cc_final: 0.9038 (tt) REVERT: B 137 ASN cc_start: 0.8467 (t0) cc_final: 0.8248 (t0) REVERT: C 278 ILE cc_start: 0.9304 (pp) cc_final: 0.8920 (mt) REVERT: D 41 MET cc_start: 0.9176 (tpp) cc_final: 0.8762 (tpp) REVERT: D 46 GLU cc_start: 0.8564 (tp30) cc_final: 0.8309 (tp30) REVERT: D 187 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8424 (p0) REVERT: D 335 ASP cc_start: 0.8913 (m-30) cc_final: 0.8703 (m-30) REVERT: E 25 ASN cc_start: 0.9289 (m-40) cc_final: 0.9017 (m110) REVERT: E 183 TYR cc_start: 0.7241 (p90) cc_final: 0.7030 (p90) REVERT: F 69 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8742 (tmm-80) REVERT: F 164 HIS cc_start: 0.8436 (t70) cc_final: 0.8082 (p-80) REVERT: G 164 HIS cc_start: 0.8592 (t-170) cc_final: 0.8123 (t70) REVERT: G 175 HIS cc_start: 0.9221 (m-70) cc_final: 0.8794 (m-70) REVERT: G 230 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.7936 (t80) outliers start: 27 outliers final: 23 residues processed: 107 average time/residue: 0.2772 time to fit residues: 50.7364 Evaluate side-chains 106 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 2.148 ------------------------------------------------------------------------------- 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 56 TYR 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 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR 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 230 PHE 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 172 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.068310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.046548 restraints weight = 85500.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048166 restraints weight = 45114.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.049192 restraints weight = 30584.385| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20554 Z= 0.112 Angle : 0.500 13.505 28001 Z= 0.250 Chirality : 0.038 0.135 3136 Planarity : 0.004 0.039 3454 Dihedral : 13.177 121.509 3226 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.41 % Allowed : 16.82 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.18), residues: 2375 helix: 1.62 (0.14), residues: 1480 sheet: -0.29 (0.38), residues: 196 loop : 0.23 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP G 267 HIS 0.022 0.001 HIS F 164 PHE 0.009 0.001 PHE B 214 TYR 0.015 0.001 TYR A 109 ARG 0.002 0.000 ARG G 153 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 1096) hydrogen bonds : angle 3.48556 ( 2975) covalent geometry : bond 0.00248 (20554) covalent geometry : angle 0.50048 (28001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6739.59 seconds wall clock time: 119 minutes 58.31 seconds (7198.31 seconds total)