Starting phenix.real_space_refine on Thu Sep 18 21:07:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g0f_50932/09_2025/9g0f_50932_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g0f_50932/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9g0f_50932/09_2025/9g0f_50932_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g0f_50932/09_2025/9g0f_50932_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g0f_50932/09_2025/9g0f_50932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g0f_50932/09_2025/9g0f_50932.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 52 5.49 5 Mg 7 5.21 5 S 56 5.16 5 C 12629 2.51 5 N 3526 2.21 5 O 3807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20077 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2672 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 13, 'TRANS': 317} Chain: "B" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "C" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "D" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "E" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "F" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "G" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "1" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.71, per 1000 atoms: 0.23 Number of scatterers: 20077 At special positions: 0 Unit cell: (96.2, 152.75, 155.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 52 15.00 Mg 7 11.99 O 3807 8.00 N 3526 7.00 C 12629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 742.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4516 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 10 sheets defined 64.3% alpha, 6.7% beta 16 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 62 through 85 Proline residue: A 80 - end of helix removed outlier: 4.182A pdb=" N SER A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.509A pdb=" N HIS A 124 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 172 through 178 removed outlier: 3.668A pdb=" N HIS A 175 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 200 removed outlier: 4.358A pdb=" N GLN A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.317A pdb=" N PHE A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.874A pdb=" N SER A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 255 Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 277 through 296 Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.581A pdb=" N ARG A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'B' and resid 8 through 14 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 62 through 83 Proline residue: B 80 - end of helix Processing helix chain 'B' and resid 105 through 117 removed outlier: 3.630A pdb=" N TYR B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 164 Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.619A pdb=" N HIS B 175 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 200 removed outlier: 3.931A pdb=" N ASP B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 215 removed outlier: 3.927A pdb=" N THR B 213 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 237 through 255 Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 266 through 273 Processing helix chain 'B' and resid 277 through 296 Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.546A pdb=" N ARG B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 332 through 344 Processing helix chain 'C' and resid 8 through 14 Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.864A pdb=" N GLU C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.560A pdb=" N GLU C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.226A pdb=" N LYS C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 164 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 183 through 200 removed outlier: 3.953A pdb=" N ASP C 187 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 215 Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 237 through 255 Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 266 through 273 Processing helix chain 'C' and resid 277 through 294 removed outlier: 3.567A pdb=" N LEU C 281 " --> pdb=" O CYS C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.740A pdb=" N ARG C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 329 removed outlier: 3.703A pdb=" N LYS C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 30 through 46 removed outlier: 3.611A pdb=" N GLU D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 79 Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 121 through 126 removed outlier: 4.062A pdb=" N LYS D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 121 through 126' Processing helix chain 'D' and resid 148 through 164 Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.645A pdb=" N HIS D 175 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 200 removed outlier: 3.727A pdb=" N LEU D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU D 192 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 237 through 255 Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 266 through 273 Processing helix chain 'D' and resid 277 through 295 removed outlier: 3.559A pdb=" N ASP D 294 " --> pdb=" O SER D 290 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.564A pdb=" N ARG D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 330 Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'E' and resid 8 through 14 Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 30 through 46 Processing helix chain 'E' and resid 62 through 79 Processing helix chain 'E' and resid 80 through 85 removed outlier: 4.873A pdb=" N GLU E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 148 through 164 Processing helix chain 'E' and resid 172 through 178 Processing helix chain 'E' and resid 183 through 200 removed outlier: 3.833A pdb=" N ASP E 187 " --> pdb=" O TYR E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 Processing helix chain 'E' and resid 218 through 224 Processing helix chain 'E' and resid 237 through 255 Processing helix chain 'E' and resid 263 through 265 No H-bonds generated for 'chain 'E' and resid 263 through 265' Processing helix chain 'E' and resid 266 through 275 Processing helix chain 'E' and resid 277 through 294 removed outlier: 3.682A pdb=" N LEU E 281 " --> pdb=" O CYS E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.743A pdb=" N ARG E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 329 Processing helix chain 'E' and resid 332 through 344 Processing helix chain 'F' and resid 8 through 14 Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 30 through 45 Processing helix chain 'F' and resid 62 through 79 removed outlier: 3.651A pdb=" N LEU F 68 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 85 removed outlier: 4.160A pdb=" N GLU F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.882A pdb=" N TYR F 109 " --> pdb=" O ASN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 125 Processing helix chain 'F' and resid 148 through 164 Processing helix chain 'F' and resid 172 through 178 removed outlier: 3.524A pdb=" N HIS F 175 " --> pdb=" O GLU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 200 removed outlier: 3.902A pdb=" N ASP F 187 " --> pdb=" O TYR F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 215 removed outlier: 3.959A pdb=" N THR F 213 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 224 Processing helix chain 'F' and resid 237 through 253 Processing helix chain 'F' and resid 266 through 273 Processing helix chain 'F' and resid 277 through 296 removed outlier: 3.544A pdb=" N LEU F 281 " --> pdb=" O CYS F 277 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG F 287 " --> pdb=" O ASP F 283 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 288 " --> pdb=" O TRP F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 308 removed outlier: 3.528A pdb=" N LYS F 307 " --> pdb=" O LYS F 303 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 327 Processing helix chain 'F' and resid 332 through 343 Processing helix chain 'G' and resid 8 through 14 Processing helix chain 'G' and resid 15 through 26 Processing helix chain 'G' and resid 30 through 46 Processing helix chain 'G' and resid 62 through 83 Proline residue: G 80 - end of helix Processing helix chain 'G' and resid 105 through 116 Processing helix chain 'G' and resid 121 through 125 removed outlier: 3.678A pdb=" N HIS G 124 " --> pdb=" O LEU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 164 Processing helix chain 'G' and resid 172 through 178 Processing helix chain 'G' and resid 184 through 200 Processing helix chain 'G' and resid 208 through 215 removed outlier: 3.758A pdb=" N LEU G 211 " --> pdb=" O THR G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 224 Processing helix chain 'G' and resid 237 through 255 Processing helix chain 'G' and resid 262 through 265 Processing helix chain 'G' and resid 266 through 273 Processing helix chain 'G' and resid 277 through 296 Processing helix chain 'G' and resid 301 through 308 removed outlier: 4.134A pdb=" N ARG G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 330 removed outlier: 3.514A pdb=" N LYS G 320 " --> pdb=" O GLN G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 344 removed outlier: 3.712A pdb=" N VAL G 336 " --> pdb=" O THR G 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 95 removed outlier: 6.721A pdb=" N VAL A 92 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP A 171 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 94 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 95 removed outlier: 3.644A pdb=" N VAL B 92 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE B 53 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLY B 207 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 55 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 56 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 95 removed outlier: 6.773A pdb=" N VAL C 92 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ASP C 171 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE C 94 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE C 168 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU C 206 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C 170 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY C 207 " --> pdb=" O VAL C 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AA5, first strand: chain 'D' and resid 91 through 95 removed outlier: 6.672A pdb=" N VAL D 92 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASP D 171 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 94 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE D 168 " --> pdb=" O CYS D 204 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU D 206 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL D 170 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE D 53 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY D 207 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL D 55 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE D 52 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE D 228 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHE D 54 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE D 230 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR D 56 " --> pdb=" O PHE D 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 134 through 135 Processing sheet with id=AA7, first strand: chain 'E' and resid 91 through 95 removed outlier: 6.638A pdb=" N VAL E 92 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASP E 171 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE E 94 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE E 168 " --> pdb=" O CYS E 204 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU E 206 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL E 170 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE E 53 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY E 207 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 55 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE E 52 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE E 228 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE E 54 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE E 230 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR E 56 " --> pdb=" O PHE E 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 133 through 135 Processing sheet with id=AA9, first strand: chain 'F' and resid 91 through 95 removed outlier: 6.722A pdb=" N VAL F 92 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASP F 171 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE F 94 " --> pdb=" O ASP F 171 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE F 168 " --> pdb=" O CYS F 204 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU F 206 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL F 170 " --> pdb=" O LEU F 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 92 through 94 removed outlier: 6.331A pdb=" N PHE G 168 " --> pdb=" O CYS G 204 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU G 206 " --> pdb=" O PHE G 168 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL G 170 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE G 53 " --> pdb=" O LEU G 205 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLY G 207 " --> pdb=" O ILE G 53 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL G 55 " --> pdb=" O GLY G 207 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 2895 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 2.52 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: 10.140 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: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.480 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.250 ------------------------------------------------------------------------------- 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 : 9.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 1.17 % Allowed : 12.69 % Favored : 86.14 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.18), residues: 2375 helix: 1.14 (0.14), residues: 1453 sheet: 0.54 (0.39), residues: 186 loop : -0.24 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 112 TYR 0.019 0.001 TYR D 37 PHE 0.015 0.001 PHE A 52 TRP 0.006 0.001 TRP G 284 HIS 0.006 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00681 (20554) covalent geometry : angle 0.97199 (28001) hydrogen bonds : bond 0.16626 ( 1096) hydrogen bonds : angle 5.64006 ( 2975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.691 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: 0.1565 time to fit residues: 29.0313 Evaluate side-chains 89 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 135 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.0050 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3492 r_free = 0.3492 target = 0.067655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.046158 restraints weight = 84587.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.047921 restraints weight = 41637.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.049047 restraints weight = 27072.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.049780 restraints weight = 20853.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.050226 restraints weight = 17757.263| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20554 Z= 0.153 Angle : 0.582 11.362 28001 Z= 0.296 Chirality : 0.041 0.300 3136 Planarity : 0.004 0.050 3454 Dihedral : 15.647 131.927 3254 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.28 % Allowed : 12.79 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.18), residues: 2375 helix: 1.17 (0.14), residues: 1485 sheet: 0.18 (0.38), residues: 196 loop : -0.08 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 327 TYR 0.016 0.001 TYR C 37 PHE 0.014 0.001 PHE B 126 TRP 0.018 0.001 TRP G 267 HIS 0.005 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00332 (20554) covalent geometry : angle 0.58156 (28001) hydrogen bonds : bond 0.04323 ( 1096) hydrogen bonds : angle 4.07642 ( 2975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 92 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.9167 (mtm) cc_final: 0.8708 (mtm) REVERT: B 94 ILE cc_start: 0.9067 (tp) cc_final: 0.8775 (tt) REVERT: B 263 LEU cc_start: 0.9614 (mt) cc_final: 0.9412 (mp) REVERT: D 41 MET cc_start: 0.9342 (tpp) cc_final: 0.8737 (tpp) REVERT: D 46 GLU cc_start: 0.8739 (tp30) cc_final: 0.8173 (tp30) REVERT: E 25 ASN cc_start: 0.9294 (m-40) cc_final: 0.8960 (m110) REVERT: E 320 LYS cc_start: 0.8990 (tppt) cc_final: 0.8758 (tppt) REVERT: F 56 TYR cc_start: 0.7591 (p90) cc_final: 0.7283 (p90) REVERT: F 216 ASN cc_start: 0.8824 (m-40) cc_final: 0.8129 (t0) REVERT: G 164 HIS cc_start: 0.7985 (t-170) cc_final: 0.7668 (t70) REVERT: G 175 HIS cc_start: 0.9020 (m-70) cc_final: 0.8537 (m-70) outliers start: 47 outliers final: 26 residues processed: 131 average time/residue: 0.1346 time to fit residues: 29.0781 Evaluate side-chains 98 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain 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 277 CYS 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 94 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 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 329 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 182 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 210 optimal weight: 20.0000 chunk 146 optimal weight: 0.1980 chunk 131 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 148 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.068848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.047318 restraints weight = 84769.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049149 restraints weight = 41100.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.050332 restraints weight = 26446.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.051079 restraints weight = 20220.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.051505 restraints weight = 17211.166| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20554 Z= 0.102 Angle : 0.501 11.311 28001 Z= 0.255 Chirality : 0.039 0.141 3136 Planarity : 0.004 0.046 3454 Dihedral : 14.024 134.072 3229 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.60 % Allowed : 13.86 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.18), residues: 2375 helix: 1.26 (0.14), residues: 1485 sheet: 0.17 (0.39), residues: 196 loop : -0.05 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.015 0.001 TYR C 37 PHE 0.010 0.001 PHE A 52 TRP 0.034 0.001 TRP G 267 HIS 0.003 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00215 (20554) covalent geometry : angle 0.50121 (28001) hydrogen bonds : bond 0.03648 ( 1096) hydrogen bonds : angle 3.77445 ( 2975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.9207 (mtm) cc_final: 0.8800 (mtm) REVERT: B 94 ILE cc_start: 0.9053 (tp) cc_final: 0.8778 (tt) REVERT: C 286 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9136 (tttt) REVERT: D 41 MET cc_start: 0.9338 (tpp) cc_final: 0.8872 (tpp) REVERT: D 46 GLU cc_start: 0.8682 (tp30) cc_final: 0.8358 (tp30) REVERT: D 187 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8502 (p0) REVERT: E 25 ASN cc_start: 0.9331 (m-40) cc_final: 0.8996 (m110) REVERT: F 56 TYR cc_start: 0.7430 (p90) cc_final: 0.6973 (p90) REVERT: F 160 LEU cc_start: 0.9593 (tp) cc_final: 0.9352 (tp) REVERT: F 164 HIS cc_start: 0.8906 (t70) cc_final: 0.8033 (t70) REVERT: F 216 ASN cc_start: 0.8755 (m-40) cc_final: 0.8001 (t0) REVERT: G 164 HIS cc_start: 0.8097 (t-170) cc_final: 0.7651 (t-170) REVERT: G 175 HIS cc_start: 0.9045 (m-70) cc_final: 0.8548 (m-70) outliers start: 33 outliers final: 16 residues processed: 116 average time/residue: 0.1204 time to fit residues: 23.3563 Evaluate side-chains 92 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 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 89 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 107 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 208 optimal weight: 20.0000 chunk 169 optimal weight: 20.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.066991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.045015 restraints weight = 86186.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.046760 restraints weight = 43351.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.047856 restraints weight = 28460.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.048493 restraints weight = 22100.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.048933 restraints weight = 19149.004| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20554 Z= 0.157 Angle : 0.538 11.606 28001 Z= 0.270 Chirality : 0.039 0.131 3136 Planarity : 0.004 0.044 3454 Dihedral : 13.701 134.137 3226 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.24 % Allowed : 14.20 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.18), residues: 2375 helix: 1.41 (0.14), residues: 1486 sheet: -0.10 (0.38), residues: 196 loop : 0.03 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 14 TYR 0.013 0.001 TYR C 37 PHE 0.013 0.001 PHE D 168 TRP 0.034 0.001 TRP G 267 HIS 0.004 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00350 (20554) covalent geometry : angle 0.53753 (28001) hydrogen bonds : bond 0.03720 ( 1096) hydrogen bonds : angle 3.79957 ( 2975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 77 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8519 (p90) REVERT: B 94 ILE cc_start: 0.9025 (tp) cc_final: 0.8751 (tt) REVERT: C 63 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7462 (mmtp) REVERT: C 286 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.8924 (tptp) REVERT: D 41 MET cc_start: 0.9352 (tpp) cc_final: 0.8809 (tpp) REVERT: D 46 GLU cc_start: 0.8813 (tp30) cc_final: 0.8409 (tp30) REVERT: D 187 ASP cc_start: 0.9254 (OUTLIER) cc_final: 0.8503 (p0) REVERT: E 25 ASN cc_start: 0.9399 (m-40) cc_final: 0.9064 (m110) REVERT: F 160 LEU cc_start: 0.9587 (tp) cc_final: 0.9352 (tp) REVERT: F 164 HIS cc_start: 0.8960 (t70) cc_final: 0.8208 (t70) REVERT: F 216 ASN cc_start: 0.8837 (m-40) cc_final: 0.8025 (t0) REVERT: G 164 HIS cc_start: 0.8278 (t-170) cc_final: 0.7786 (t70) REVERT: G 175 HIS cc_start: 0.9161 (m-70) cc_final: 0.8590 (m-70) outliers start: 46 outliers final: 25 residues processed: 115 average time/residue: 0.1321 time to fit residues: 25.1149 Evaluate side-chains 98 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 63 LYS Chi-restraints excluded: chain C residue 94 ILE 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 148 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 90 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 229 optimal weight: 8.9990 chunk 230 optimal weight: 8.9990 chunk 214 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.066655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.044726 restraints weight = 85902.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.046417 restraints weight = 43238.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.047501 restraints weight = 28505.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.048201 restraints weight = 22171.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.048600 restraints weight = 19070.564| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20554 Z= 0.159 Angle : 0.535 12.345 28001 Z= 0.267 Chirality : 0.039 0.177 3136 Planarity : 0.004 0.043 3454 Dihedral : 13.622 132.294 3226 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.75 % Allowed : 14.97 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.18), residues: 2375 helix: 1.44 (0.14), residues: 1486 sheet: -0.21 (0.38), residues: 196 loop : 0.02 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 86 TYR 0.012 0.001 TYR C 37 PHE 0.012 0.001 PHE D 168 TRP 0.036 0.001 TRP G 267 HIS 0.004 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00353 (20554) covalent geometry : angle 0.53486 (28001) hydrogen bonds : bond 0.03621 ( 1096) hydrogen bonds : angle 3.76733 ( 2975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 71 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9544 (t0) cc_final: 0.9107 (t0) REVERT: A 198 MET cc_start: 0.8988 (mtm) cc_final: 0.8603 (mtm) REVERT: B 56 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8484 (p90) REVERT: B 94 ILE cc_start: 0.9003 (tp) cc_final: 0.8737 (tt) REVERT: C 63 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7829 (mttm) REVERT: C 286 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.8905 (tptp) REVERT: D 41 MET cc_start: 0.9320 (tpp) cc_final: 0.8527 (tpp) REVERT: D 187 ASP cc_start: 0.9266 (OUTLIER) cc_final: 0.8507 (p0) REVERT: E 25 ASN cc_start: 0.9408 (m-40) cc_final: 0.9079 (m110) REVERT: F 160 LEU cc_start: 0.9596 (tp) cc_final: 0.9375 (tp) REVERT: F 164 HIS cc_start: 0.8986 (t70) cc_final: 0.8286 (t70) REVERT: F 216 ASN cc_start: 0.8893 (m-40) cc_final: 0.8081 (t0) REVERT: G 164 HIS cc_start: 0.8358 (t-170) cc_final: 0.7871 (t70) REVERT: G 175 HIS cc_start: 0.9212 (m-70) cc_final: 0.8660 (m-70) outliers start: 36 outliers final: 25 residues processed: 104 average time/residue: 0.1186 time to fit residues: 21.0212 Evaluate side-chains 98 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 63 LYS Chi-restraints excluded: chain C residue 94 ILE 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 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 206 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.067850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.045961 restraints weight = 85388.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.047564 restraints weight = 45267.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.048610 restraints weight = 30898.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.049280 restraints weight = 24502.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.049643 restraints weight = 21271.581| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20554 Z= 0.126 Angle : 0.506 13.165 28001 Z= 0.253 Chirality : 0.038 0.147 3136 Planarity : 0.004 0.042 3454 Dihedral : 13.508 127.542 3226 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.14 % Allowed : 14.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.18), residues: 2375 helix: 1.52 (0.14), residues: 1480 sheet: -0.25 (0.37), residues: 196 loop : 0.14 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 153 TYR 0.014 0.001 TYR C 37 PHE 0.011 0.001 PHE E 168 TRP 0.044 0.001 TRP G 267 HIS 0.003 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00278 (20554) covalent geometry : angle 0.50648 (28001) hydrogen bonds : bond 0.03457 ( 1096) hydrogen bonds : angle 3.65022 ( 2975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 76 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9574 (t0) cc_final: 0.9156 (t0) REVERT: A 198 MET cc_start: 0.8937 (mtm) cc_final: 0.8566 (mtm) REVERT: B 56 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8284 (p90) REVERT: B 94 ILE cc_start: 0.9287 (tp) cc_final: 0.9056 (tt) REVERT: C 63 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8263 (mttm) REVERT: D 41 MET cc_start: 0.9260 (tpp) cc_final: 0.8858 (tpp) REVERT: D 187 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8460 (p0) REVERT: E 25 ASN cc_start: 0.9259 (m-40) cc_final: 0.8982 (m110) REVERT: F 164 HIS cc_start: 0.8748 (t70) cc_final: 0.8430 (t70) REVERT: F 216 ASN cc_start: 0.8632 (m-40) cc_final: 0.7893 (t0) REVERT: G 164 HIS cc_start: 0.8504 (t-170) cc_final: 0.7999 (t70) REVERT: G 175 HIS cc_start: 0.9291 (m-70) cc_final: 0.8743 (m-70) outliers start: 44 outliers final: 23 residues processed: 114 average time/residue: 0.1364 time to fit residues: 26.4695 Evaluate side-chains 98 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 A residue 318 MET 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 63 LYS Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 185 LEU 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 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 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 28 optimal weight: 9.9990 chunk 68 optimal weight: 0.0670 chunk 171 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 overall best weight: 1.6126 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.067327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.045131 restraints weight = 85510.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.046701 restraints weight = 46152.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.047706 restraints weight = 31819.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.048362 restraints weight = 25427.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.048732 restraints weight = 22216.155| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2414 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= 0.133 Angle : 0.518 13.991 28001 Z= 0.257 Chirality : 0.038 0.164 3136 Planarity : 0.004 0.041 3454 Dihedral : 13.496 125.601 3226 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.04 % Allowed : 15.02 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.18), residues: 2375 helix: 1.53 (0.14), residues: 1480 sheet: -0.29 (0.37), residues: 196 loop : 0.14 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 131 TYR 0.014 0.001 TYR C 37 PHE 0.009 0.001 PHE C 168 TRP 0.043 0.001 TRP G 267 HIS 0.003 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00297 (20554) covalent geometry : angle 0.51760 (28001) hydrogen bonds : bond 0.03419 ( 1096) hydrogen bonds : angle 3.63499 ( 2975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 79 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9581 (t0) cc_final: 0.9164 (t0) REVERT: A 198 MET cc_start: 0.8895 (mtm) cc_final: 0.8518 (mtm) REVERT: B 56 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8291 (p90) REVERT: B 94 ILE cc_start: 0.9300 (tp) cc_final: 0.9069 (tt) REVERT: B 137 ASN cc_start: 0.8425 (t0) cc_final: 0.8170 (t0) REVERT: C 63 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8383 (mttm) REVERT: D 41 MET cc_start: 0.9257 (tpp) cc_final: 0.8850 (tpp) REVERT: D 187 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8479 (p0) REVERT: D 335 ASP cc_start: 0.8913 (m-30) cc_final: 0.8689 (m-30) REVERT: E 25 ASN cc_start: 0.9259 (m-40) cc_final: 0.8985 (m110) REVERT: F 164 HIS cc_start: 0.8766 (t70) cc_final: 0.8527 (t70) REVERT: G 164 HIS cc_start: 0.8547 (t-170) cc_final: 0.8044 (t70) REVERT: G 175 HIS cc_start: 0.9317 (m-70) cc_final: 0.8801 (m-70) REVERT: G 178 LYS cc_start: 0.7286 (mptt) cc_final: 0.7021 (mttm) REVERT: G 230 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7880 (t80) outliers start: 42 outliers final: 30 residues processed: 116 average time/residue: 0.1269 time to fit residues: 25.1352 Evaluate side-chains 108 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 318 MET 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 63 LYS 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 252 GLN Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 218 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 83 optimal weight: 0.0000 chunk 170 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.068060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.046197 restraints weight = 85117.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.047815 restraints weight = 44971.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.048854 restraints weight = 30572.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.049492 restraints weight = 24245.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.049900 restraints weight = 21131.928| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20554 Z= 0.105 Angle : 0.503 13.372 28001 Z= 0.249 Chirality : 0.038 0.171 3136 Planarity : 0.003 0.041 3454 Dihedral : 13.450 123.740 3226 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.51 % Allowed : 15.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.18), residues: 2375 helix: 1.54 (0.14), residues: 1480 sheet: -0.24 (0.38), residues: 196 loop : 0.17 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 69 TYR 0.014 0.001 TYR C 37 PHE 0.009 0.001 PHE A 52 TRP 0.045 0.001 TRP G 267 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00231 (20554) covalent geometry : angle 0.50312 (28001) hydrogen bonds : bond 0.03303 ( 1096) hydrogen bonds : angle 3.54797 ( 2975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9577 (t0) cc_final: 0.9165 (t0) REVERT: A 198 MET cc_start: 0.8905 (mtm) cc_final: 0.8551 (mtm) REVERT: B 94 ILE cc_start: 0.9284 (tp) cc_final: 0.9042 (tt) REVERT: B 137 ASN cc_start: 0.8398 (t0) cc_final: 0.8140 (t0) REVERT: C 63 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8398 (mttm) REVERT: D 41 MET cc_start: 0.9210 (tpp) cc_final: 0.8837 (tpp) REVERT: D 187 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8457 (p0) REVERT: D 335 ASP cc_start: 0.8873 (m-30) cc_final: 0.8660 (m-30) REVERT: E 25 ASN cc_start: 0.9254 (m-40) cc_final: 0.8983 (m110) REVERT: G 164 HIS cc_start: 0.8546 (t-170) cc_final: 0.8051 (t70) REVERT: G 175 HIS cc_start: 0.9314 (m-70) cc_final: 0.8854 (m-70) REVERT: G 178 LYS cc_start: 0.7316 (mptt) cc_final: 0.7073 (mttm) REVERT: G 230 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7886 (t80) outliers start: 31 outliers final: 24 residues processed: 109 average time/residue: 0.1290 time to fit residues: 23.6769 Evaluate side-chains 103 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 260 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 94 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 228 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.068129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.046222 restraints weight = 85380.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.047853 restraints weight = 45328.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.048900 restraints weight = 30804.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.049559 restraints weight = 24390.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049912 restraints weight = 21264.520| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20554 Z= 0.116 Angle : 0.519 14.743 28001 Z= 0.254 Chirality : 0.038 0.215 3136 Planarity : 0.004 0.040 3454 Dihedral : 13.398 122.806 3226 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.65 % Allowed : 15.90 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.18), residues: 2375 helix: 1.56 (0.14), residues: 1480 sheet: -0.24 (0.38), residues: 196 loop : 0.18 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 327 TYR 0.014 0.001 TYR C 37 PHE 0.008 0.001 PHE B 214 TRP 0.048 0.001 TRP G 267 HIS 0.021 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00258 (20554) covalent geometry : angle 0.51881 (28001) hydrogen bonds : bond 0.03282 ( 1096) hydrogen bonds : angle 3.56586 ( 2975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9584 (t0) cc_final: 0.9172 (t0) REVERT: A 198 MET cc_start: 0.8904 (mtm) cc_final: 0.8546 (mtm) REVERT: B 94 ILE cc_start: 0.9281 (tp) cc_final: 0.9038 (tt) REVERT: B 137 ASN cc_start: 0.8430 (t0) cc_final: 0.8199 (t0) REVERT: C 63 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8403 (mttm) REVERT: D 41 MET cc_start: 0.9228 (tpp) cc_final: 0.8845 (tpp) REVERT: D 187 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8440 (p0) REVERT: D 335 ASP cc_start: 0.8883 (m-30) cc_final: 0.8668 (m-30) REVERT: E 25 ASN cc_start: 0.9279 (m-40) cc_final: 0.9003 (m110) REVERT: G 164 HIS cc_start: 0.8585 (t-170) cc_final: 0.8103 (t70) REVERT: G 175 HIS cc_start: 0.9342 (m-70) cc_final: 0.8848 (m-70) REVERT: G 178 LYS cc_start: 0.7342 (mptt) cc_final: 0.7048 (mttm) REVERT: G 230 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7912 (t80) outliers start: 34 outliers final: 27 residues processed: 113 average time/residue: 0.1326 time to fit residues: 25.5444 Evaluate side-chains 107 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 A residue 318 MET 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 63 LYS Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 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 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 186 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 173 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.067614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.045732 restraints weight = 85548.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.047370 restraints weight = 45271.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048401 restraints weight = 30655.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.049042 restraints weight = 24297.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.049409 restraints weight = 21200.229| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20554 Z= 0.132 Angle : 0.532 14.163 28001 Z= 0.262 Chirality : 0.039 0.203 3136 Planarity : 0.004 0.040 3454 Dihedral : 13.334 122.311 3226 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.65 % Allowed : 16.24 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.18), residues: 2375 helix: 1.56 (0.14), residues: 1480 sheet: -0.28 (0.38), residues: 196 loop : 0.18 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 14 TYR 0.014 0.001 TYR C 37 PHE 0.009 0.001 PHE C 168 TRP 0.051 0.001 TRP G 267 HIS 0.022 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00295 (20554) covalent geometry : angle 0.53195 (28001) hydrogen bonds : bond 0.03366 ( 1096) hydrogen bonds : angle 3.60490 ( 2975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9584 (t0) cc_final: 0.9172 (t0) REVERT: B 56 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.8266 (p90) REVERT: B 94 ILE cc_start: 0.9288 (tp) cc_final: 0.9052 (tt) REVERT: B 137 ASN cc_start: 0.8464 (t0) cc_final: 0.8261 (t0) REVERT: C 63 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8442 (mttm) REVERT: D 41 MET cc_start: 0.9279 (tpp) cc_final: 0.8786 (tpp) REVERT: D 187 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8443 (p0) REVERT: D 335 ASP cc_start: 0.8874 (m-30) cc_final: 0.8659 (m-30) REVERT: E 25 ASN cc_start: 0.9293 (m-40) cc_final: 0.9022 (m110) REVERT: F 164 HIS cc_start: 0.8471 (t70) cc_final: 0.8072 (p-80) REVERT: G 164 HIS cc_start: 0.8604 (t-170) cc_final: 0.8141 (t70) REVERT: G 175 HIS cc_start: 0.9356 (m-70) cc_final: 0.8793 (m-70) REVERT: G 178 LYS cc_start: 0.7376 (mptt) cc_final: 0.7042 (mttm) REVERT: G 230 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.7966 (t80) outliers start: 34 outliers final: 27 residues processed: 110 average time/residue: 0.1267 time to fit residues: 23.8022 Evaluate side-chains 109 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 A residue 318 MET 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 63 LYS Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 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 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 146 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.068090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.046295 restraints weight = 85522.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.047925 restraints weight = 45022.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.048990 restraints weight = 30299.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.049561 restraints weight = 24019.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049996 restraints weight = 21125.833| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20554 Z= 0.111 Angle : 0.520 14.866 28001 Z= 0.256 Chirality : 0.038 0.180 3136 Planarity : 0.003 0.040 3454 Dihedral : 13.234 121.131 3226 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.46 % Allowed : 16.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.18), residues: 2375 helix: 1.57 (0.14), residues: 1480 sheet: -0.28 (0.38), residues: 196 loop : 0.18 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 327 TYR 0.016 0.001 TYR A 109 PHE 0.008 0.001 PHE B 214 TRP 0.050 0.001 TRP G 267 HIS 0.021 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00245 (20554) covalent geometry : angle 0.52014 (28001) hydrogen bonds : bond 0.03254 ( 1096) hydrogen bonds : angle 3.56647 ( 2975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3556.73 seconds wall clock time: 62 minutes 30.56 seconds (3750.56 seconds total)