Starting phenix.real_space_refine on Sat Jun 6 19:18:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sgk_54871/06_2026/9sgk_54871_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sgk_54871/06_2026/9sgk_54871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sgk_54871/06_2026/9sgk_54871_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sgk_54871/06_2026/9sgk_54871_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sgk_54871/06_2026/9sgk_54871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sgk_54871/06_2026/9sgk_54871.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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: 7 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9585 2.51 5 N 2575 2.21 5 O 2920 1.98 5 H 14945 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30145 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 227 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "C" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 227 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "D" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 227 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "E" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 227 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "F" Number of atoms: 5774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5774 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 5774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5774 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 5774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5774 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 5774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5774 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 5774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5774 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 227 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.57, per 1000 atoms: 0.18 Number of scatterers: 30145 At special positions: 0 Unit cell: (97.37, 93.73, 197.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2920 8.00 N 2575 7.00 C 9585 6.00 H 14945 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 754.1 milliseconds 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 40 sheets defined 49.8% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'B' and resid 7 through 16 removed outlier: 4.151A pdb=" N LEU B 11 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 12 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 9 No H-bonds generated for 'chain 'C' and resid 7 through 9' Processing helix chain 'C' and resid 10 through 17 removed outlier: 3.872A pdb=" N GLN C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 14 removed outlier: 3.503A pdb=" N GLN D 14 " --> pdb=" O SER D 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 17 removed outlier: 3.860A pdb=" N PHE E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 removed outlier: 4.041A pdb=" N LYS F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.680A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.040A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET F 123 " --> pdb=" O MET F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 removed outlier: 3.706A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA F 144 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 194 removed outlier: 3.945A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.952A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS F 215 " --> pdb=" O ASP F 211 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 252 through 260 removed outlier: 3.816A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 261 through 268 Proline residue: F 264 - end of helix removed outlier: 3.606A pdb=" N GLY F 268 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 285 removed outlier: 3.561A pdb=" N THR F 278 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS F 284 " --> pdb=" O ASN F 280 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.990A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 337 through 347 removed outlier: 3.536A pdb=" N GLY F 343 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 363 Processing helix chain 'F' and resid 366 through 372 Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 93 removed outlier: 4.597A pdb=" N LYS G 84 " --> pdb=" O ASP G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.544A pdb=" N GLU G 100 " --> pdb=" O ALA G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.772A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 removed outlier: 3.875A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER G 145 " --> pdb=" O SER G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 175 removed outlier: 3.521A pdb=" N ILE G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 175' Processing helix chain 'G' and resid 181 through 194 removed outlier: 3.820A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 217 removed outlier: 3.806A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS G 217 " --> pdb=" O LYS G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 231 removed outlier: 3.615A pdb=" N ALA G 228 " --> pdb=" O GLU G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 260 removed outlier: 3.691A pdb=" N ARG G 256 " --> pdb=" O ASN G 252 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Proline residue: G 258 - end of helix No H-bonds generated for 'chain 'G' and resid 252 through 260' Processing helix chain 'G' and resid 261 through 268 Proline residue: G 264 - end of helix Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 286 through 288 No H-bonds generated for 'chain 'G' and resid 286 through 288' Processing helix chain 'G' and resid 289 through 295 removed outlier: 3.693A pdb=" N ALA G 295 " --> pdb=" O LYS G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 306 removed outlier: 4.171A pdb=" N TYR G 306 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 removed outlier: 3.806A pdb=" N ARG G 312 " --> pdb=" O GLY G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 347 Processing helix chain 'G' and resid 351 through 356 removed outlier: 4.058A pdb=" N TRP G 356 " --> pdb=" O GLN G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 364 Processing helix chain 'G' and resid 366 through 372 Processing helix chain 'H' and resid 55 through 61 removed outlier: 3.993A pdb=" N GLN H 59 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER H 60 " --> pdb=" O ASP H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 92 removed outlier: 3.800A pdb=" N LYS H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP H 86 " --> pdb=" O MET H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 4.013A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET H 123 " --> pdb=" O MET H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 145 removed outlier: 3.759A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 175 removed outlier: 3.812A pdb=" N ILE H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 172 through 175' Processing helix chain 'H' and resid 181 through 193 Processing helix chain 'H' and resid 194 through 197 Processing helix chain 'H' and resid 202 through 217 removed outlier: 3.531A pdb=" N ARG H 206 " --> pdb=" O THR H 202 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS H 213 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS H 215 " --> pdb=" O ASP H 211 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS H 217 " --> pdb=" O LYS H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 231 removed outlier: 3.509A pdb=" N ALA H 231 " --> pdb=" O MET H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 257 removed outlier: 3.922A pdb=" N CYS H 257 " --> pdb=" O GLU H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 268 Proline residue: H 264 - end of helix Processing helix chain 'H' and resid 273 through 284 removed outlier: 3.711A pdb=" N ILE H 282 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET H 283 " --> pdb=" O TYR H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 295 removed outlier: 3.765A pdb=" N LEU H 293 " --> pdb=" O ILE H 289 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA H 295 " --> pdb=" O LYS H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 305 Processing helix chain 'H' and resid 308 through 321 removed outlier: 3.522A pdb=" N ARG H 312 " --> pdb=" O GLY H 308 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 337 through 347 Processing helix chain 'H' and resid 366 through 372 Processing helix chain 'I' and resid 55 through 61 Processing helix chain 'I' and resid 78 through 93 removed outlier: 3.703A pdb=" N GLU I 83 " --> pdb=" O TRP I 79 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS I 84 " --> pdb=" O ASP I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 101 removed outlier: 3.517A pdb=" N HIS I 101 " --> pdb=" O PRO I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.557A pdb=" N MET I 123 " --> pdb=" O MET I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 146 removed outlier: 3.625A pdb=" N SER I 145 " --> pdb=" O SER I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 175 Processing helix chain 'I' and resid 181 through 194 removed outlier: 3.651A pdb=" N LEU I 185 " --> pdb=" O ALA I 181 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR I 194 " --> pdb=" O MET I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'I' and resid 202 through 217 removed outlier: 3.892A pdb=" N GLU I 207 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS I 215 " --> pdb=" O ASP I 211 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS I 217 " --> pdb=" O LYS I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 231 Processing helix chain 'I' and resid 252 through 257 removed outlier: 3.830A pdb=" N CYS I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 268 Proline residue: I 264 - end of helix Processing helix chain 'I' and resid 273 through 285 removed outlier: 3.697A pdb=" N CYS I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 295 removed outlier: 4.016A pdb=" N ALA I 295 " --> pdb=" O LYS I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 305 Processing helix chain 'I' and resid 308 through 321 removed outlier: 3.761A pdb=" N ARG I 312 " --> pdb=" O GLY I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 336 No H-bonds generated for 'chain 'I' and resid 334 through 336' Processing helix chain 'I' and resid 337 through 347 Processing helix chain 'I' and resid 351 through 356 removed outlier: 3.831A pdb=" N GLN I 354 " --> pdb=" O THR I 351 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP I 356 " --> pdb=" O GLN I 353 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 366 removed outlier: 3.527A pdb=" N GLU I 364 " --> pdb=" O GLN I 360 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA I 365 " --> pdb=" O GLU I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 4.001A pdb=" N ARG I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS I 373 " --> pdb=" O ILE I 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 368 through 373' Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.520A pdb=" N GLN J 59 " --> pdb=" O GLY J 55 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 93 removed outlier: 4.148A pdb=" N LYS J 84 " --> pdb=" O ASP J 80 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP J 86 " --> pdb=" O MET J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 101 Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.597A pdb=" N ARG J 116 " --> pdb=" O PRO J 112 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET J 123 " --> pdb=" O MET J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 144 removed outlier: 3.987A pdb=" N LEU J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR J 143 " --> pdb=" O VAL J 139 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA J 144 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 175 Processing helix chain 'J' and resid 181 through 194 removed outlier: 4.219A pdb=" N THR J 194 " --> pdb=" O MET J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 217 removed outlier: 3.986A pdb=" N GLU J 207 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL J 209 " --> pdb=" O GLU J 205 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE J 212 " --> pdb=" O ILE J 208 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS J 217 " --> pdb=" O LYS J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 231 removed outlier: 3.546A pdb=" N ALA J 228 " --> pdb=" O GLU J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 260 removed outlier: 3.671A pdb=" N ARG J 256 " --> pdb=" O ASN J 252 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS J 257 " --> pdb=" O GLU J 253 " (cutoff:3.500A) Proline residue: J 258 - end of helix No H-bonds generated for 'chain 'J' and resid 252 through 260' Processing helix chain 'J' and resid 261 through 268 Proline residue: J 264 - end of helix Processing helix chain 'J' and resid 273 through 284 removed outlier: 3.504A pdb=" N TYR J 279 " --> pdb=" O HIS J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 295 removed outlier: 3.888A pdb=" N ALA J 295 " --> pdb=" O LYS J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 306 removed outlier: 4.023A pdb=" N TYR J 306 " --> pdb=" O THR J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 321 removed outlier: 3.704A pdb=" N ARG J 312 " --> pdb=" O GLY J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 336 No H-bonds generated for 'chain 'J' and resid 334 through 336' Processing helix chain 'J' and resid 337 through 347 Processing helix chain 'J' and resid 348 through 355 removed outlier: 6.064A pdb=" N THR J 351 " --> pdb=" O SER J 348 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN J 354 " --> pdb=" O THR J 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 366 removed outlier: 4.192A pdb=" N GLU J 364 " --> pdb=" O GLN J 360 " (cutoff:3.500A) Processing helix chain 'J' and resid 367 through 372 Processing helix chain 'P' and resid 8 through 19 removed outlier: 3.889A pdb=" N ILE P 12 " --> pdb=" O VAL P 8 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG P 17 " --> pdb=" O GLU P 13 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN P 19 " --> pdb=" O PHE P 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 8 through 12 removed outlier: 3.707A pdb=" N LYS F 18 " --> pdb=" O ASP F 11 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE F 31 " --> pdb=" O VAL F 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'F' and resid 105 through 107 removed outlier: 6.319A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 131 through 132 removed outlier: 3.520A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 152 through 155 removed outlier: 3.950A pdb=" N VAL F 152 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL F 163 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET F 176 " --> pdb=" O ASN F 162 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 165 through 166 Processing sheet with id=AA8, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'G' and resid 16 through 19 removed outlier: 3.635A pdb=" N PHE G 31 " --> pdb=" O VAL G 17 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.547A pdb=" N VAL G 35 " --> pdb=" O LYS G 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 105 through 107 Processing sheet with id=AB3, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AB4, first strand: chain 'G' and resid 150 through 155 removed outlier: 3.853A pdb=" N GLY G 150 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL G 152 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL G 163 " --> pdb=" O VAL G 152 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 150 through 155 removed outlier: 3.853A pdb=" N GLY G 150 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL G 152 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL G 163 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET G 176 " --> pdb=" O ASN G 162 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 238 through 241 removed outlier: 3.757A pdb=" N ILE G 250 " --> pdb=" O LYS G 238 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR G 240 " --> pdb=" O ILE G 248 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 297 through 298 removed outlier: 6.797A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'H' and resid 16 through 19 removed outlier: 3.712A pdb=" N PHE H 31 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA H 19 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA H 29 " --> pdb=" O ALA H 19 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.877A pdb=" N VAL H 35 " --> pdb=" O LYS H 68 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS H 68 " --> pdb=" O VAL H 35 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AC2, first strand: chain 'H' and resid 105 through 107 removed outlier: 3.565A pdb=" N ALA H 135 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 131 through 132 Processing sheet with id=AC4, first strand: chain 'H' and resid 149 through 155 removed outlier: 3.524A pdb=" N GLY H 150 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL H 152 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL H 163 " --> pdb=" O VAL H 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 149 through 155 removed outlier: 3.524A pdb=" N GLY H 150 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL H 152 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL H 163 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET H 176 " --> pdb=" O ASN H 162 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 238 through 241 removed outlier: 3.686A pdb=" N ILE H 250 " --> pdb=" O LYS H 238 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.797A pdb=" N LYS I 18 " --> pdb=" O ASP I 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.615A pdb=" N TYR I 53 " --> pdb=" O GLY I 36 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY I 36 " --> pdb=" O TYR I 53 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'I' and resid 105 through 107 removed outlier: 3.548A pdb=" N ALA I 135 " --> pdb=" O LEU I 105 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 131 through 132 Processing sheet with id=AD3, first strand: chain 'I' and resid 176 through 178 removed outlier: 3.681A pdb=" N MET I 176 " --> pdb=" O ASN I 162 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL I 152 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER I 155 " --> pdb=" O SER I 300 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN I 297 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 165 through 166 removed outlier: 3.547A pdb=" N TYR I 166 " --> pdb=" O TYR I 169 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 238 through 241 Processing sheet with id=AD6, first strand: chain 'J' and resid 8 through 12 removed outlier: 3.609A pdb=" N LYS J 18 " --> pdb=" O ASP J 11 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.598A pdb=" N VAL J 35 " --> pdb=" O LYS J 68 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AD9, first strand: chain 'J' and resid 105 through 107 Processing sheet with id=AE1, first strand: chain 'J' and resid 131 through 132 removed outlier: 3.621A pdb=" N MET J 132 " --> pdb=" O ILE J 357 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 160 through 163 removed outlier: 3.600A pdb=" N VAL J 163 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL J 152 " --> pdb=" O VAL J 163 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASN J 297 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 165 through 166 Processing sheet with id=AE4, first strand: chain 'J' and resid 240 through 241 551 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.34 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14880 1.03 - 1.23: 118 1.23 - 1.43: 6347 1.43 - 1.62: 8935 1.62 - 1.82: 185 Bond restraints: 30465 Sorted by residual: bond pdb=" CE1 HIC H 73 " pdb=" HE1 HIC H 73 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" CE1 HIC F 73 " pdb=" HE1 HIC F 73 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" CE1 HIC J 73 " pdb=" HE1 HIC J 73 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" CE1 HIC G 73 " pdb=" HE1 HIC G 73 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" CE1 HIC I 73 " pdb=" HE1 HIC I 73 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.77e+01 ... (remaining 30460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 54644 1.96 - 3.91: 336 3.91 - 5.87: 58 5.87 - 7.82: 6 7.82 - 9.78: 1 Bond angle restraints: 55045 Sorted by residual: angle pdb=" CB MET J 47 " pdb=" CG MET J 47 " pdb=" SD MET J 47 " ideal model delta sigma weight residual 112.70 122.48 -9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" CB MET I 283 " pdb=" CG MET I 283 " pdb=" SD MET I 283 " ideal model delta sigma weight residual 112.70 120.11 -7.41 3.00e+00 1.11e-01 6.10e+00 angle pdb=" N HIC G 73 " pdb=" CA HIC G 73 " pdb=" CB HIC G 73 " ideal model delta sigma weight residual 110.50 114.42 -3.92 1.70e+00 3.46e-01 5.30e+00 angle pdb=" C TYR G 91 " pdb=" N ASN G 92 " pdb=" CA ASN G 92 " ideal model delta sigma weight residual 122.08 118.68 3.40 1.53e+00 4.27e-01 4.94e+00 angle pdb=" CA GLY J 13 " pdb=" C GLY J 13 " pdb=" O GLY J 13 " ideal model delta sigma weight residual 122.76 120.34 2.42 1.12e+00 7.97e-01 4.68e+00 ... (remaining 55040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.76: 13328 23.76 - 47.53: 800 47.53 - 71.29: 185 71.29 - 95.05: 36 95.05 - 118.81: 1 Dihedral angle restraints: 14350 sinusoidal: 7915 harmonic: 6435 Sorted by residual: dihedral pdb=" O2A ADP F 402 " pdb=" O3A ADP F 402 " pdb=" PA ADP F 402 " pdb=" PB ADP F 402 " ideal model delta sinusoidal sigma weight residual -60.00 58.81 -118.81 1 2.00e+01 2.50e-03 3.56e+01 dihedral pdb=" O2A ADP J 402 " pdb=" O3A ADP J 402 " pdb=" PA ADP J 402 " pdb=" PB ADP J 402 " ideal model delta sinusoidal sigma weight residual -60.00 30.56 -90.55 1 2.00e+01 2.50e-03 2.42e+01 dihedral pdb=" C5' ADP H 402 " pdb=" O5' ADP H 402 " pdb=" PA ADP H 402 " pdb=" O2A ADP H 402 " ideal model delta sinusoidal sigma weight residual -60.00 -143.92 83.93 1 2.00e+01 2.50e-03 2.15e+01 ... (remaining 14347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1409 0.029 - 0.059: 615 0.059 - 0.088: 145 0.088 - 0.117: 146 0.117 - 0.147: 25 Chirality restraints: 2340 Sorted by residual: chirality pdb=" CA VAL G 129 " pdb=" N VAL G 129 " pdb=" C VAL G 129 " pdb=" CB VAL G 129 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE F 165 " pdb=" N ILE F 165 " pdb=" C ILE F 165 " pdb=" CB ILE F 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA VAL H 129 " pdb=" N VAL H 129 " pdb=" C VAL H 129 " pdb=" CB VAL H 129 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2337 not shown) Planarity restraints: 4505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS G 257 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO G 258 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO G 258 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 258 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 306 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO H 307 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO H 307 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 307 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 321 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO I 322 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO I 322 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 322 " 0.017 5.00e-02 4.00e+02 ... (remaining 4502 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1850 2.20 - 2.80: 60924 2.80 - 3.40: 77944 3.40 - 4.00: 101174 4.00 - 4.60: 159355 Nonbonded interactions: 401247 Sorted by model distance: nonbonded pdb=" OD1 ASN H 128 " pdb=" HZ1 LYS H 359 " model vdw 1.598 2.450 nonbonded pdb=" O ARG F 116 " pdb=" HG1 THR F 120 " model vdw 1.600 2.450 nonbonded pdb=" OE1 GLU F 334 " pdb=" H GLU F 334 " model vdw 1.602 2.450 nonbonded pdb=" O ILE G 122 " pdb=" HG1 THR G 126 " model vdw 1.604 2.450 nonbonded pdb=" O GLN J 314 " pdb=" HG1 THR J 318 " model vdw 1.605 2.450 ... (remaining 401242 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.160 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.600 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.003 0.057 15520 Z= 0.156 Angle : 0.587 9.780 21045 Z= 0.289 Chirality : 0.042 0.147 2340 Planarity : 0.003 0.062 2690 Dihedral : 15.536 118.812 5790 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.06 % Allowed : 13.31 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.19), residues: 1885 helix: -1.28 (0.19), residues: 701 sheet: -2.06 (0.29), residues: 335 loop : -1.18 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 290 TYR 0.008 0.001 TYR F 294 PHE 0.007 0.001 PHE H 375 TRP 0.008 0.001 TRP G 340 HIS 0.003 0.001 HIS H 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (15520) covalent geometry : angle 0.58702 / 0.29 (21045) hydrogen bonds : bond 0.32199 / 20.45 ( 545) hydrogen bonds : angle 9.42946 / 6.55 ( 1392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 123 MET cc_start: 0.8949 (mmt) cc_final: 0.8551 (mmm) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.2394 time to fit residues: 49.5311 Evaluate side-chains 126 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 205 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 12 ASN G 162 ASN I 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.088415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.073520 restraints weight = 102838.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.076729 restraints weight = 42031.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.078749 restraints weight = 22897.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.079994 restraints weight = 15147.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080772 restraints weight = 11471.104| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15520 Z= 0.115 Angle : 0.586 6.201 21045 Z= 0.292 Chirality : 0.043 0.147 2340 Planarity : 0.004 0.053 2690 Dihedral : 7.362 110.782 2158 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.86 % Allowed : 12.33 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.20), residues: 1885 helix: -0.33 (0.20), residues: 741 sheet: -1.89 (0.28), residues: 345 loop : -0.95 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 183 TYR 0.011 0.001 TYR I 143 PHE 0.009 0.001 PHE G 223 TRP 0.008 0.001 TRP J 86 HIS 0.004 0.001 HIS G 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (15520) covalent geometry : angle 0.58628 / 0.29 (21045) hydrogen bonds : bond 0.05185 / 3.30 ( 545) hydrogen bonds : angle 5.53711 / 3.83 ( 1392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 260 THR cc_start: 0.9089 (m) cc_final: 0.8845 (p) REVERT: J 83 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8207 (tm-30) outliers start: 14 outliers final: 11 residues processed: 144 average time/residue: 0.2373 time to fit residues: 54.2541 Evaluate side-chains 137 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 211 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 66 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 13 optimal weight: 0.2980 chunk 189 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.086681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.071983 restraints weight = 104637.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.075115 restraints weight = 42719.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.077090 restraints weight = 23313.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.078304 restraints weight = 15428.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.079070 restraints weight = 11686.201| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15520 Z= 0.197 Angle : 0.601 6.408 21045 Z= 0.298 Chirality : 0.044 0.150 2340 Planarity : 0.004 0.049 2690 Dihedral : 7.312 112.517 2155 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.86 % Allowed : 13.50 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.20), residues: 1885 helix: -0.33 (0.19), residues: 741 sheet: -2.02 (0.28), residues: 345 loop : -1.10 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 9 TYR 0.009 0.001 TYR G 240 PHE 0.010 0.001 PHE H 375 TRP 0.010 0.001 TRP H 79 HIS 0.003 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (15520) covalent geometry : angle 0.60050 / 0.30 (21045) hydrogen bonds : bond 0.04821 / 3.08 ( 545) hydrogen bonds : angle 5.18485 / 3.58 ( 1392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 138 average time/residue: 0.2327 time to fit residues: 50.5438 Evaluate side-chains 138 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain J residue 106 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 121 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 14 optimal weight: 0.3980 chunk 111 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.072951 restraints weight = 103373.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.076070 restraints weight = 42585.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.078046 restraints weight = 23360.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.079291 restraints weight = 15530.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080060 restraints weight = 11747.196| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15520 Z= 0.140 Angle : 0.559 6.252 21045 Z= 0.272 Chirality : 0.043 0.143 2340 Planarity : 0.003 0.044 2690 Dihedral : 7.049 105.974 2155 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.35 % Allowed : 13.80 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.20), residues: 1885 helix: -0.09 (0.20), residues: 741 sheet: -1.95 (0.28), residues: 345 loop : -1.03 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 9 TYR 0.008 0.001 TYR F 166 PHE 0.008 0.001 PHE H 375 TRP 0.010 0.001 TRP I 86 HIS 0.006 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (15520) covalent geometry : angle 0.55858 / 0.27 (21045) hydrogen bonds : bond 0.03760 / 2.40 ( 545) hydrogen bonds : angle 4.70520 / 3.24 ( 1392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 260 THR cc_start: 0.9066 (m) cc_final: 0.8834 (p) REVERT: J 83 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8135 (tm-30) outliers start: 22 outliers final: 16 residues processed: 150 average time/residue: 0.2379 time to fit residues: 55.9228 Evaluate side-chains 146 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 106 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 176 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.087685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.073072 restraints weight = 103430.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.076190 restraints weight = 43056.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.078171 restraints weight = 23711.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.079414 restraints weight = 15788.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080214 restraints weight = 11926.530| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15520 Z= 0.182 Angle : 0.584 6.309 21045 Z= 0.287 Chirality : 0.044 0.145 2340 Planarity : 0.004 0.040 2690 Dihedral : 7.129 111.196 2155 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.09 % Allowed : 13.62 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.20), residues: 1885 helix: -0.10 (0.20), residues: 741 sheet: -2.00 (0.28), residues: 345 loop : -1.11 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 9 TYR 0.009 0.001 TYR G 240 PHE 0.010 0.001 PHE H 375 TRP 0.009 0.001 TRP H 79 HIS 0.005 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (15520) covalent geometry : angle 0.58435 / 0.29 (21045) hydrogen bonds : bond 0.03968 / 2.53 ( 545) hydrogen bonds : angle 4.68792 / 3.22 ( 1392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 290 ARG cc_start: 0.5318 (ptt-90) cc_final: 0.4994 (ptt90) REVERT: I 260 THR cc_start: 0.9053 (m) cc_final: 0.8813 (p) REVERT: J 83 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8154 (tm-30) outliers start: 34 outliers final: 25 residues processed: 158 average time/residue: 0.2406 time to fit residues: 59.7951 Evaluate side-chains 156 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 111 ASN Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 304 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 186 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.086313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.071589 restraints weight = 104548.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.074714 restraints weight = 42453.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.076697 restraints weight = 23133.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.077933 restraints weight = 15323.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.078712 restraints weight = 11551.215| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15520 Z= 0.198 Angle : 0.597 6.249 21045 Z= 0.294 Chirality : 0.044 0.145 2340 Planarity : 0.004 0.037 2690 Dihedral : 7.158 114.906 2155 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.02 % Allowed : 14.48 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.20), residues: 1885 helix: -0.10 (0.20), residues: 741 sheet: -2.04 (0.28), residues: 345 loop : -1.16 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 9 TYR 0.010 0.001 TYR G 240 PHE 0.011 0.001 PHE H 375 TRP 0.017 0.002 TRP I 86 HIS 0.005 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (15520) covalent geometry : angle 0.59657 / 0.29 (21045) hydrogen bonds : bond 0.03950 / 2.52 ( 545) hydrogen bonds : angle 4.66667 / 3.20 ( 1392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 237 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7482 (mt-10) REVERT: G 290 ARG cc_start: 0.5245 (ptt-90) cc_final: 0.4917 (ptt90) REVERT: I 246 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7823 (tp-100) REVERT: J 83 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8193 (tm-30) outliers start: 33 outliers final: 28 residues processed: 162 average time/residue: 0.2406 time to fit residues: 61.6338 Evaluate side-chains 161 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 304 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 28 optimal weight: 8.9990 chunk 131 optimal weight: 0.0040 chunk 63 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.087453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.072923 restraints weight = 103960.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.076053 restraints weight = 43149.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.078035 restraints weight = 23754.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.079271 restraints weight = 15787.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.080060 restraints weight = 11930.834| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15520 Z= 0.171 Angle : 0.580 6.184 21045 Z= 0.283 Chirality : 0.043 0.144 2340 Planarity : 0.004 0.035 2690 Dihedral : 7.002 114.060 2155 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 1.96 % Allowed : 14.66 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.20), residues: 1885 helix: 0.01 (0.20), residues: 741 sheet: -1.99 (0.28), residues: 345 loop : -1.14 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 9 TYR 0.009 0.001 TYR G 279 PHE 0.009 0.001 PHE H 375 TRP 0.016 0.001 TRP I 86 HIS 0.005 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (15520) covalent geometry : angle 0.58030 / 0.28 (21045) hydrogen bonds : bond 0.03701 / 2.35 ( 545) hydrogen bonds : angle 4.52968 / 3.11 ( 1392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 GLN cc_start: 0.5984 (mm-40) cc_final: 0.4934 (mm-40) REVERT: G 45 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8446 (p) REVERT: G 237 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7485 (mt-10) REVERT: G 290 ARG cc_start: 0.5313 (ptt-90) cc_final: 0.4978 (ptt90) REVERT: I 246 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7794 (tp-100) REVERT: J 83 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8158 (tm-30) REVERT: J 325 MET cc_start: 0.8609 (mmp) cc_final: 0.8350 (tpp) outliers start: 32 outliers final: 31 residues processed: 161 average time/residue: 0.2367 time to fit residues: 59.9695 Evaluate side-chains 165 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 111 ASN Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 304 THR Chi-restraints excluded: chain J residue 324 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 78 optimal weight: 0.0470 chunk 175 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 132 optimal weight: 0.0470 overall best weight: 1.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.088577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.073846 restraints weight = 103466.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.077096 restraints weight = 41793.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.079135 restraints weight = 22635.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.080392 restraints weight = 14901.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.081189 restraints weight = 11204.465| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15520 Z= 0.090 Angle : 0.536 6.300 21045 Z= 0.254 Chirality : 0.042 0.141 2340 Planarity : 0.003 0.033 2690 Dihedral : 6.546 104.094 2155 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.17 % Allowed : 15.52 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.21), residues: 1885 helix: 0.45 (0.21), residues: 731 sheet: -1.79 (0.29), residues: 345 loop : -0.94 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 9 TYR 0.008 0.001 TYR F 166 PHE 0.005 0.001 PHE H 352 TRP 0.018 0.001 TRP I 86 HIS 0.005 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (15520) covalent geometry : angle 0.53552 / 0.25 (21045) hydrogen bonds : bond 0.02863 / 1.83 ( 545) hydrogen bonds : angle 4.17760 / 2.87 ( 1392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 GLN cc_start: 0.6161 (mm-40) cc_final: 0.5117 (mm-40) REVERT: G 186 THR cc_start: 0.8927 (m) cc_final: 0.8670 (m) REVERT: G 290 ARG cc_start: 0.5203 (ptt-90) cc_final: 0.4915 (ptt90) REVERT: I 246 GLN cc_start: 0.8059 (tp-100) cc_final: 0.7793 (tp-100) REVERT: I 260 THR cc_start: 0.9063 (m) cc_final: 0.8830 (p) REVERT: J 83 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8108 (tm-30) REVERT: J 325 MET cc_start: 0.8612 (mmp) cc_final: 0.8361 (tpp) outliers start: 19 outliers final: 17 residues processed: 158 average time/residue: 0.2510 time to fit residues: 62.3037 Evaluate side-chains 154 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 304 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 86 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 155 optimal weight: 0.2980 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.088269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.073764 restraints weight = 103443.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.076935 restraints weight = 41876.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.078935 restraints weight = 22757.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.080174 restraints weight = 15017.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.080960 restraints weight = 11300.383| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15520 Z= 0.104 Angle : 0.541 6.527 21045 Z= 0.256 Chirality : 0.042 0.138 2340 Planarity : 0.003 0.033 2690 Dihedral : 6.440 103.242 2155 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.04 % Allowed : 15.95 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.21), residues: 1885 helix: 0.53 (0.21), residues: 731 sheet: -1.73 (0.29), residues: 345 loop : -0.90 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 9 TYR 0.008 0.001 TYR F 166 PHE 0.005 0.001 PHE H 375 TRP 0.018 0.001 TRP I 86 HIS 0.004 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (15520) covalent geometry : angle 0.54147 / 0.26 (21045) hydrogen bonds : bond 0.02952 / 1.88 ( 545) hydrogen bonds : angle 4.14284 / 2.85 ( 1392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 GLN cc_start: 0.6115 (mm-40) cc_final: 0.5090 (mm-40) REVERT: G 186 THR cc_start: 0.8960 (m) cc_final: 0.8710 (m) REVERT: G 290 ARG cc_start: 0.5210 (ptt-90) cc_final: 0.4924 (ptt90) REVERT: H 358 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8034 (p) REVERT: I 246 GLN cc_start: 0.8049 (tp-100) cc_final: 0.7779 (tp-100) REVERT: I 260 THR cc_start: 0.9069 (m) cc_final: 0.8841 (p) REVERT: J 83 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8120 (tm-30) REVERT: J 325 MET cc_start: 0.8642 (mmp) cc_final: 0.8396 (tpp) outliers start: 17 outliers final: 16 residues processed: 147 average time/residue: 0.2454 time to fit residues: 56.3937 Evaluate side-chains 151 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 304 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 135 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 153 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.086189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.071902 restraints weight = 105079.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.074919 restraints weight = 43364.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.076846 restraints weight = 23898.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.078029 restraints weight = 15908.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.078799 restraints weight = 12080.936| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15520 Z= 0.200 Angle : 0.602 7.466 21045 Z= 0.294 Chirality : 0.044 0.143 2340 Planarity : 0.004 0.035 2690 Dihedral : 6.670 112.654 2155 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.17 % Allowed : 15.77 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.20), residues: 1885 helix: 0.27 (0.20), residues: 731 sheet: -1.78 (0.29), residues: 335 loop : -1.10 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 9 TYR 0.010 0.001 TYR G 279 PHE 0.011 0.001 PHE H 375 TRP 0.016 0.002 TRP I 86 HIS 0.004 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (15520) covalent geometry : angle 0.60240 / 0.29 (21045) hydrogen bonds : bond 0.03749 / 2.39 ( 545) hydrogen bonds : angle 4.44051 / 3.05 ( 1392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 GLN cc_start: 0.6022 (mm-40) cc_final: 0.5011 (mm-40) REVERT: G 290 ARG cc_start: 0.5376 (ptt-90) cc_final: 0.5102 (ptt90) REVERT: I 246 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7786 (tp-100) REVERT: J 83 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8175 (tm-30) REVERT: J 325 MET cc_start: 0.8631 (mmp) cc_final: 0.8397 (tpp) outliers start: 19 outliers final: 18 residues processed: 144 average time/residue: 0.2589 time to fit residues: 57.9463 Evaluate side-chains 148 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 304 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 53 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.072704 restraints weight = 104169.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.075884 restraints weight = 41749.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.077882 restraints weight = 22550.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.079126 restraints weight = 14825.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.079913 restraints weight = 11136.251| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15520 Z= 0.132 Angle : 0.559 7.265 21045 Z= 0.268 Chirality : 0.042 0.142 2340 Planarity : 0.003 0.033 2690 Dihedral : 6.491 108.538 2155 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.10 % Allowed : 15.83 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.20), residues: 1885 helix: 0.40 (0.20), residues: 731 sheet: -1.72 (0.29), residues: 335 loop : -1.04 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 9 TYR 0.008 0.001 TYR F 166 PHE 0.007 0.001 PHE H 375 TRP 0.017 0.001 TRP I 86 HIS 0.004 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (15520) covalent geometry : angle 0.55855 / 0.27 (21045) hydrogen bonds : bond 0.03234 / 2.06 ( 545) hydrogen bonds : angle 4.25751 / 2.93 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3756.83 seconds wall clock time: 65 minutes 7.71 seconds (3907.71 seconds total)