Starting phenix.real_space_refine on Sat Aug 23 11:32:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjm_50506/08_2025/9fjm_50506.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjm_50506/08_2025/9fjm_50506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fjm_50506/08_2025/9fjm_50506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjm_50506/08_2025/9fjm_50506.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fjm_50506/08_2025/9fjm_50506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjm_50506/08_2025/9fjm_50506.map" } resolution = 3.65 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= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7417 2.51 5 N 1975 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11772 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2803 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 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: "B" Number of atoms: 2847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2847 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 1 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: "C" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "D" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.59, per 1000 atoms: 0.30 Number of scatterers: 11772 At special positions: 0 Unit cell: (97.68, 80.08, 154.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 12 15.00 Mg 4 11.99 O 2280 8.00 N 1975 7.00 C 7417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " " TRP K 1 " - " ALA K 7 " " DTH K 4 " - " ALA K 3 " Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 540.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH K 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 24 sheets defined 49.7% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.596A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.736A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.621A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.614A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.618A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.614A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.708A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.635A pdb=" N MET A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.367A pdb=" N LYS A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.522A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.763A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 removed outlier: 3.648A pdb=" N ASP A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.708A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.715A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.696A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.034A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.504A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.729A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.989A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.585A pdb=" N MET B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.797A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Proline residue: B 258 - end of helix removed outlier: 4.755A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.533A pdb=" N TYR B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.533A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.552A pdb=" N ILE B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.636A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.985A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.546A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.544A pdb=" N LEU C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.829A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.971A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.658A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 4.063A pdb=" N ALA C 174 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 171 through 175' Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.535A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.652A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 232 removed outlier: 3.569A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.726A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.517A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.717A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 366 removed outlier: 3.784A pdb=" N SER C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.529A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.589A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.579A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.000A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.633A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.940A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.802A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.073A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.249A pdb=" N LYS D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.796A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.594A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.524A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 366 removed outlier: 3.527A pdb=" N ASP D 363 " --> pdb=" O LYS D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 4.363A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.585A pdb=" N PHE A 31 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 106 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.856A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.865A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 165 through 166 removed outlier: 3.907A pdb=" N TYR A 166 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.547A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.622A pdb=" N PHE B 31 " --> pdb=" O CYS B 17 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 133 " --> pdb=" O VAL B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.502A pdb=" N LEU B 176 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.685A pdb=" N TYR B 166 " --> pdb=" O TYR B 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.886A pdb=" N PHE C 31 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR C 106 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.530A pdb=" N ILE C 250 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 10 removed outlier: 3.819A pdb=" N THR D 106 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR D 133 " --> pdb=" O VAL D 103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 16 through 19 removed outlier: 3.812A pdb=" N PHE D 31 " --> pdb=" O CYS D 17 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.628A pdb=" N LYS D 68 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.637A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 176 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.637A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 removed outlier: 3.653A pdb=" N LYS D 238 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE D 250 " --> pdb=" O LYS D 238 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1230 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: 1.96 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3806 1.35 - 1.46: 2759 1.46 - 1.58: 5303 1.58 - 1.70: 12 1.70 - 1.82: 144 Bond restraints: 12024 Sorted by residual: bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.00e+00 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.00e+00 bond pdb=" CB LYS B 291 " pdb=" CG LYS B 291 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.02e-01 ... (remaining 12019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 16032 1.85 - 3.70: 227 3.70 - 5.55: 42 5.55 - 7.40: 14 7.40 - 9.25: 5 Bond angle restraints: 16320 Sorted by residual: angle pdb=" CB MET A 355 " pdb=" CG MET A 355 " pdb=" SD MET A 355 " ideal model delta sigma weight residual 112.70 121.95 -9.25 3.00e+00 1.11e-01 9.51e+00 angle pdb=" CB LYS B 291 " pdb=" CG LYS B 291 " pdb=" CD LYS B 291 " ideal model delta sigma weight residual 111.30 118.00 -6.70 2.30e+00 1.89e-01 8.48e+00 angle pdb=" CA LEU A 242 " pdb=" CB LEU A 242 " pdb=" CG LEU A 242 " ideal model delta sigma weight residual 116.30 125.30 -9.00 3.50e+00 8.16e-02 6.62e+00 angle pdb=" CB MET D 325 " pdb=" CG MET D 325 " pdb=" SD MET D 325 " ideal model delta sigma weight residual 112.70 105.04 7.66 3.00e+00 1.11e-01 6.51e+00 angle pdb=" CB MET C 355 " pdb=" CG MET C 355 " pdb=" SD MET C 355 " ideal model delta sigma weight residual 112.70 120.27 -7.57 3.00e+00 1.11e-01 6.37e+00 ... (remaining 16315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.20: 6392 20.20 - 40.40: 684 40.40 - 60.60: 127 60.60 - 80.80: 29 80.80 - 101.00: 10 Dihedral angle restraints: 7242 sinusoidal: 2937 harmonic: 4305 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 41.00 -101.00 1 2.00e+01 2.50e-03 2.86e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 39.71 -99.71 1 2.00e+01 2.50e-03 2.80e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 8.07 -68.07 1 2.00e+01 2.50e-03 1.50e+01 ... (remaining 7239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1263 0.037 - 0.074: 382 0.074 - 0.110: 148 0.110 - 0.147: 18 0.147 - 0.184: 5 Chirality restraints: 1816 Sorted by residual: chirality pdb=" CA HYP H 6 " pdb=" N HYP H 6 " pdb=" C HYP H 6 " pdb=" CB HYP H 6 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA HYP I 6 " pdb=" N HYP I 6 " pdb=" C HYP I 6 " pdb=" CB HYP I 6 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CA HYP J 6 " pdb=" N HYP J 6 " pdb=" C HYP J 6 " pdb=" CB HYP J 6 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 1813 not shown) Planarity restraints: 2072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N TRP J 1 " -0.025 2.00e-02 2.50e+03 4.27e-02 1.83e+01 pdb=" CA ALA J 7 " -0.021 2.00e-02 2.50e+03 pdb=" C ALA J 7 " 0.074 2.00e-02 2.50e+03 pdb=" O ALA J 7 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 129 " 0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO C 130 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 130 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 130 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 257 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO D 258 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 258 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 258 " 0.025 5.00e-02 4.00e+02 ... (remaining 2069 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 37 2.39 - 3.02: 6454 3.02 - 3.65: 17430 3.65 - 4.27: 25917 4.27 - 4.90: 44047 Nonbonded interactions: 93885 Sorted by model distance: nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.766 3.620 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.782 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.785 3.620 nonbonded pdb=" CD1 TRP K 1 " pdb=" SG CYS K 5 " model vdw 1.808 3.620 nonbonded pdb="MG MG B 402 " pdb=" O2 PO4 B 403 " model vdw 2.050 2.170 ... (remaining 93880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 6 through 39 or resid 50 through 374 or resid 401 through \ 403)) selection = (chain 'C' and (resid 6 through 39 or resid 50 through 374 or resid 401 through \ 403)) selection = (chain 'D' and (resid 6 through 39 or resid 50 through 374 or resid 401 through \ 403)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 7.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.320 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.002 0.031 12032 Z= 0.104 Angle : 0.594 16.244 16344 Z= 0.280 Chirality : 0.042 0.184 1816 Planarity : 0.004 0.051 2064 Dihedral : 16.752 100.999 4458 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.24 % Allowed : 22.26 % Favored : 77.50 % 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 aren not related in a simple way. whole: -0.30 (0.23), residues: 1439 helix: -0.69 (0.22), residues: 521 sheet: -0.73 (0.39), residues: 193 loop : 0.58 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 372 TYR 0.012 0.001 TYR D 362 PHE 0.006 0.001 PHE B 223 TRP 0.020 0.001 TRP B 86 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00233 (12024) covalent geometry : angle 0.57368 (16320) hydrogen bonds : bond 0.30713 ( 466) hydrogen bonds : angle 8.49159 ( 1230) link_TRANS : bond 0.00468 ( 8) link_TRANS : angle 4.09484 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: D 132 MET cc_start: 0.6366 (ttt) cc_final: 0.6127 (ttt) REVERT: D 325 MET cc_start: 0.7436 (ttp) cc_final: 0.6949 (ttp) outliers start: 3 outliers final: 1 residues processed: 139 average time/residue: 0.0965 time to fit residues: 20.6885 Evaluate side-chains 131 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 12 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105397 restraints weight = 18765.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.108578 restraints weight = 11577.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110874 restraints weight = 8068.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112541 restraints weight = 6070.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113754 restraints weight = 4836.437| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12032 Z= 0.258 Angle : 0.701 7.635 16344 Z= 0.341 Chirality : 0.049 0.223 1816 Planarity : 0.005 0.054 2064 Dihedral : 8.179 112.879 1709 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.92 % Allowed : 19.68 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.22), residues: 1439 helix: -0.10 (0.21), residues: 561 sheet: -0.73 (0.33), residues: 242 loop : 0.24 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.014 0.002 TYR C 362 PHE 0.014 0.002 PHE D 90 TRP 0.022 0.002 TRP H 1 HIS 0.006 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00616 (12024) covalent geometry : angle 0.70159 (16320) hydrogen bonds : bond 0.05191 ( 466) hydrogen bonds : angle 5.46260 ( 1230) link_TRANS : bond 0.00270 ( 8) link_TRANS : angle 0.46133 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 140 time to evaluate : 0.447 Fit side-chains REVERT: C 283 MET cc_start: 0.8348 (tpp) cc_final: 0.6949 (mpp) REVERT: C 292 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7582 (t0) REVERT: D 9 VAL cc_start: 0.9042 (t) cc_final: 0.8761 (m) outliers start: 61 outliers final: 40 residues processed: 180 average time/residue: 0.0867 time to fit residues: 24.6091 Evaluate side-chains 167 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 15 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 138 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN B 101 HIS D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106077 restraints weight = 18632.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109410 restraints weight = 11313.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.111774 restraints weight = 7748.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.113502 restraints weight = 5772.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.114739 restraints weight = 4564.101| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12032 Z= 0.134 Angle : 0.596 7.970 16344 Z= 0.280 Chirality : 0.045 0.206 1816 Planarity : 0.004 0.050 2064 Dihedral : 7.969 110.487 1708 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.95 % Allowed : 20.65 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.23), residues: 1439 helix: 0.24 (0.22), residues: 563 sheet: -0.69 (0.33), residues: 244 loop : 0.26 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 372 TYR 0.015 0.001 TYR D 294 PHE 0.012 0.001 PHE A 223 TRP 0.009 0.001 TRP A 86 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00319 (12024) covalent geometry : angle 0.59660 (16320) hydrogen bonds : bond 0.03962 ( 466) hydrogen bonds : angle 4.98694 ( 1230) link_TRANS : bond 0.00124 ( 8) link_TRANS : angle 0.27796 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 0.461 Fit side-chains REVERT: A 123 MET cc_start: 0.7829 (mtp) cc_final: 0.7547 (mtp) REVERT: A 207 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6766 (tm-30) REVERT: B 153 MET cc_start: 0.7603 (tmm) cc_final: 0.7106 (tmt) REVERT: C 62 ARG cc_start: 0.8875 (ptt-90) cc_final: 0.8605 (ptt-90) REVERT: C 283 MET cc_start: 0.8306 (tpp) cc_final: 0.6952 (mpp) REVERT: D 9 VAL cc_start: 0.8989 (t) cc_final: 0.8731 (m) REVERT: D 107 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.6276 (tm-30) REVERT: D 132 MET cc_start: 0.6675 (ttt) cc_final: 0.6433 (ttt) REVERT: D 294 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.6553 (t80) REVERT: D 346 LEU cc_start: 0.8662 (tp) cc_final: 0.8334 (tt) outliers start: 49 outliers final: 28 residues processed: 173 average time/residue: 0.0945 time to fit residues: 25.0819 Evaluate side-chains 154 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS D 12 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.126554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.108424 restraints weight = 18545.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111823 restraints weight = 11082.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.114225 restraints weight = 7542.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115922 restraints weight = 5578.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117148 restraints weight = 4396.846| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12032 Z= 0.156 Angle : 0.604 8.988 16344 Z= 0.284 Chirality : 0.045 0.215 1816 Planarity : 0.004 0.047 2064 Dihedral : 7.929 112.301 1708 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.44 % Allowed : 20.32 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.23), residues: 1439 helix: 0.41 (0.22), residues: 560 sheet: -0.84 (0.32), residues: 256 loop : 0.21 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 372 TYR 0.012 0.001 TYR D 294 PHE 0.019 0.001 PHE A 223 TRP 0.017 0.001 TRP A 86 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00376 (12024) covalent geometry : angle 0.60457 (16320) hydrogen bonds : bond 0.03637 ( 466) hydrogen bonds : angle 4.78066 ( 1230) link_TRANS : bond 0.00163 ( 8) link_TRANS : angle 0.26465 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 133 time to evaluate : 0.486 Fit side-chains REVERT: A 104 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8405 (tt) REVERT: A 207 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6872 (tm-30) REVERT: A 353 GLN cc_start: 0.8216 (mm110) cc_final: 0.7612 (tm-30) REVERT: B 153 MET cc_start: 0.7610 (tmm) cc_final: 0.7151 (tmt) REVERT: B 167 GLU cc_start: 0.7853 (tp30) cc_final: 0.7650 (tp30) REVERT: B 259 GLU cc_start: 0.7854 (tp30) cc_final: 0.7449 (tp30) REVERT: B 328 LYS cc_start: 0.7951 (tptt) cc_final: 0.7701 (tttp) REVERT: C 62 ARG cc_start: 0.8928 (ptt-90) cc_final: 0.8709 (ptt-90) REVERT: D 9 VAL cc_start: 0.9020 (t) cc_final: 0.8764 (m) REVERT: D 294 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.6413 (t80) outliers start: 55 outliers final: 44 residues processed: 173 average time/residue: 0.0909 time to fit residues: 24.3997 Evaluate side-chains 173 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 127 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 12 ASN D 12 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.126679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108458 restraints weight = 18616.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111858 restraints weight = 11127.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114240 restraints weight = 7561.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.115965 restraints weight = 5610.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117213 restraints weight = 4419.467| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12032 Z= 0.157 Angle : 0.608 9.059 16344 Z= 0.283 Chirality : 0.045 0.224 1816 Planarity : 0.004 0.045 2064 Dihedral : 7.911 112.396 1708 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 5.65 % Allowed : 19.68 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.23), residues: 1439 helix: 0.46 (0.23), residues: 561 sheet: -0.85 (0.32), residues: 254 loop : 0.25 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 372 TYR 0.012 0.001 TYR D 294 PHE 0.014 0.001 PHE A 223 TRP 0.016 0.001 TRP A 86 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00379 (12024) covalent geometry : angle 0.60806 (16320) hydrogen bonds : bond 0.03484 ( 466) hydrogen bonds : angle 4.67605 ( 1230) link_TRANS : bond 0.00157 ( 8) link_TRANS : angle 0.26935 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 133 time to evaluate : 0.551 Fit side-chains REVERT: A 104 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8407 (tt) REVERT: A 190 MET cc_start: 0.7050 (tpp) cc_final: 0.6720 (tpp) REVERT: A 207 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6831 (tm-30) REVERT: A 259 GLU cc_start: 0.6981 (tp30) cc_final: 0.6772 (tp30) REVERT: A 353 GLN cc_start: 0.8228 (mm110) cc_final: 0.7667 (tm-30) REVERT: B 16 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7812 (ptp) REVERT: B 132 MET cc_start: 0.7768 (tpp) cc_final: 0.7353 (tpt) REVERT: B 153 MET cc_start: 0.7590 (tmm) cc_final: 0.7136 (tmt) REVERT: B 167 GLU cc_start: 0.7878 (tp30) cc_final: 0.7660 (tp30) REVERT: B 259 GLU cc_start: 0.7843 (tp30) cc_final: 0.7416 (tp30) REVERT: B 328 LYS cc_start: 0.7955 (tptt) cc_final: 0.7711 (tttp) REVERT: C 123 MET cc_start: 0.7235 (tpp) cc_final: 0.6939 (mmt) REVERT: C 125 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6988 (mt-10) REVERT: D 9 VAL cc_start: 0.9026 (t) cc_final: 0.8769 (m) REVERT: D 151 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7831 (pt) REVERT: D 294 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.6350 (t80) outliers start: 70 outliers final: 52 residues processed: 187 average time/residue: 0.0897 time to fit residues: 26.2137 Evaluate side-chains 184 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 128 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS C 12 ASN D 12 ASN D 252 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.108266 restraints weight = 18696.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111647 restraints weight = 11208.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114041 restraints weight = 7631.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.115731 restraints weight = 5675.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116941 restraints weight = 4484.957| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12032 Z= 0.156 Angle : 0.603 9.388 16344 Z= 0.281 Chirality : 0.045 0.230 1816 Planarity : 0.004 0.045 2064 Dihedral : 7.883 112.482 1708 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.56 % Allowed : 20.65 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.23), residues: 1439 helix: 0.57 (0.23), residues: 561 sheet: -0.92 (0.32), residues: 264 loop : 0.27 (0.27), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 372 TYR 0.013 0.001 TYR D 294 PHE 0.014 0.001 PHE A 223 TRP 0.013 0.001 TRP A 86 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00375 (12024) covalent geometry : angle 0.60347 (16320) hydrogen bonds : bond 0.03402 ( 466) hydrogen bonds : angle 4.64257 ( 1230) link_TRANS : bond 0.00149 ( 8) link_TRANS : angle 0.29142 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 131 time to evaluate : 0.573 Fit side-chains REVERT: A 104 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8466 (tt) REVERT: A 190 MET cc_start: 0.7023 (tpp) cc_final: 0.6752 (tpp) REVERT: A 205 GLU cc_start: 0.6840 (mp0) cc_final: 0.6312 (pm20) REVERT: A 207 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6838 (tm-30) REVERT: A 353 GLN cc_start: 0.8192 (mm110) cc_final: 0.7682 (tm-30) REVERT: B 16 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7802 (ptp) REVERT: B 132 MET cc_start: 0.7768 (tpp) cc_final: 0.7450 (tpt) REVERT: B 153 MET cc_start: 0.7598 (tmm) cc_final: 0.7118 (tmt) REVERT: B 167 GLU cc_start: 0.7859 (tp30) cc_final: 0.7637 (tp30) REVERT: B 328 LYS cc_start: 0.7967 (tptt) cc_final: 0.7730 (tttp) REVERT: C 125 GLU cc_start: 0.7265 (mm-30) cc_final: 0.7013 (mt-10) REVERT: D 9 VAL cc_start: 0.9046 (t) cc_final: 0.8758 (m) REVERT: D 151 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7813 (pt) REVERT: D 256 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7790 (ttt180) REVERT: D 294 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.6294 (t80) outliers start: 69 outliers final: 51 residues processed: 185 average time/residue: 0.0912 time to fit residues: 26.2630 Evaluate side-chains 179 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 123 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 105 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 110 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 144 optimal weight: 0.0000 chunk 123 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN D 12 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.127544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.110321 restraints weight = 18550.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113436 restraints weight = 11562.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115652 restraints weight = 8045.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117205 restraints weight = 6068.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118353 restraints weight = 4860.342| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12032 Z= 0.132 Angle : 0.593 9.884 16344 Z= 0.276 Chirality : 0.045 0.231 1816 Planarity : 0.004 0.044 2064 Dihedral : 7.813 111.521 1708 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.76 % Allowed : 21.85 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.23), residues: 1439 helix: 0.65 (0.23), residues: 561 sheet: -0.85 (0.32), residues: 266 loop : 0.24 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 372 TYR 0.013 0.001 TYR D 294 PHE 0.018 0.001 PHE A 223 TRP 0.015 0.001 TRP A 86 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00317 (12024) covalent geometry : angle 0.59367 (16320) hydrogen bonds : bond 0.03173 ( 466) hydrogen bonds : angle 4.56611 ( 1230) link_TRANS : bond 0.00126 ( 8) link_TRANS : angle 0.28688 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 124 time to evaluate : 0.485 Fit side-chains REVERT: A 205 GLU cc_start: 0.6746 (mp0) cc_final: 0.6320 (pm20) REVERT: A 207 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6782 (tm-30) REVERT: A 353 GLN cc_start: 0.8128 (mm110) cc_final: 0.7704 (tm-30) REVERT: B 16 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7767 (ptp) REVERT: B 132 MET cc_start: 0.7728 (tpp) cc_final: 0.7434 (tpt) REVERT: B 153 MET cc_start: 0.7583 (tmm) cc_final: 0.7113 (tmt) REVERT: B 259 GLU cc_start: 0.7820 (tp30) cc_final: 0.7417 (tp30) REVERT: B 328 LYS cc_start: 0.7977 (tptt) cc_final: 0.7749 (tttp) REVERT: D 9 VAL cc_start: 0.9008 (t) cc_final: 0.8747 (m) REVERT: D 151 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7793 (pt) REVERT: D 256 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7782 (ttt180) REVERT: D 294 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6226 (t80) outliers start: 59 outliers final: 44 residues processed: 172 average time/residue: 0.0941 time to fit residues: 24.8760 Evaluate side-chains 167 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 124 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.0670 chunk 114 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 49 GLN D 12 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.111380 restraints weight = 18546.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.114484 restraints weight = 11566.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116724 restraints weight = 8072.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118298 restraints weight = 6064.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119453 restraints weight = 4831.631| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12032 Z= 0.114 Angle : 0.585 10.070 16344 Z= 0.272 Chirality : 0.044 0.230 1816 Planarity : 0.004 0.043 2064 Dihedral : 7.713 110.181 1708 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.19 % Allowed : 22.18 % Favored : 73.63 % 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 aren not related in a simple way. whole: 0.24 (0.23), residues: 1439 helix: 0.75 (0.23), residues: 562 sheet: -0.83 (0.32), residues: 272 loop : 0.30 (0.27), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 372 TYR 0.014 0.001 TYR C 362 PHE 0.025 0.001 PHE A 223 TRP 0.016 0.001 TRP A 86 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00269 (12024) covalent geometry : angle 0.58545 (16320) hydrogen bonds : bond 0.02965 ( 466) hydrogen bonds : angle 4.47310 ( 1230) link_TRANS : bond 0.00104 ( 8) link_TRANS : angle 0.28592 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 124 time to evaluate : 0.316 Fit side-chains REVERT: A 207 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6788 (tm-30) REVERT: A 353 GLN cc_start: 0.8092 (mm110) cc_final: 0.7703 (tm-30) REVERT: B 16 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7773 (ptp) REVERT: B 82 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7719 (tpt) REVERT: B 132 MET cc_start: 0.7645 (tpp) cc_final: 0.7297 (tpt) REVERT: B 153 MET cc_start: 0.7580 (tmm) cc_final: 0.7140 (tmt) REVERT: B 259 GLU cc_start: 0.7833 (tp30) cc_final: 0.7397 (tp30) REVERT: B 328 LYS cc_start: 0.8035 (tptt) cc_final: 0.7808 (tttp) REVERT: D 9 VAL cc_start: 0.8984 (t) cc_final: 0.8775 (m) REVERT: D 151 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7788 (pt) REVERT: D 256 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7780 (ttt180) REVERT: D 294 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.6134 (t80) outliers start: 52 outliers final: 38 residues processed: 163 average time/residue: 0.0942 time to fit residues: 23.5193 Evaluate side-chains 161 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 38 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 43 optimal weight: 0.0470 chunk 89 optimal weight: 0.9980 chunk 131 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN D 12 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110837 restraints weight = 18402.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113918 restraints weight = 11507.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116096 restraints weight = 8036.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.117632 restraints weight = 6059.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118778 restraints weight = 4845.218| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12032 Z= 0.129 Angle : 0.601 10.235 16344 Z= 0.280 Chirality : 0.045 0.233 1816 Planarity : 0.004 0.042 2064 Dihedral : 7.696 110.757 1708 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.52 % Allowed : 22.10 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.23), residues: 1439 helix: 0.87 (0.23), residues: 548 sheet: -0.98 (0.31), residues: 283 loop : 0.31 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 372 TYR 0.013 0.001 TYR D 294 PHE 0.023 0.001 PHE A 223 TRP 0.023 0.001 TRP A 86 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00307 (12024) covalent geometry : angle 0.60162 (16320) hydrogen bonds : bond 0.03052 ( 466) hydrogen bonds : angle 4.45488 ( 1230) link_TRANS : bond 0.00120 ( 8) link_TRANS : angle 0.31136 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 125 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6791 (tm-30) REVERT: A 353 GLN cc_start: 0.8114 (mm110) cc_final: 0.7711 (tm-30) REVERT: B 16 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7755 (ptp) REVERT: B 132 MET cc_start: 0.7669 (tpp) cc_final: 0.7321 (tpt) REVERT: B 153 MET cc_start: 0.7593 (tmm) cc_final: 0.7139 (tmt) REVERT: B 259 GLU cc_start: 0.7794 (tp30) cc_final: 0.7453 (tp30) REVERT: B 328 LYS cc_start: 0.8046 (tptt) cc_final: 0.7825 (tttp) REVERT: D 151 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7804 (pt) REVERT: D 256 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7802 (ttt180) REVERT: D 294 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.6142 (t80) outliers start: 56 outliers final: 43 residues processed: 169 average time/residue: 0.0869 time to fit residues: 22.6819 Evaluate side-chains 167 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 120 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 19 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111398 restraints weight = 18659.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114505 restraints weight = 11752.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116686 restraints weight = 8196.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118194 restraints weight = 6200.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.119365 restraints weight = 4969.986| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12032 Z= 0.139 Angle : 0.616 12.693 16344 Z= 0.285 Chirality : 0.045 0.235 1816 Planarity : 0.004 0.043 2064 Dihedral : 7.692 110.679 1708 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.35 % Allowed : 22.50 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.23), residues: 1439 helix: 0.81 (0.23), residues: 559 sheet: -1.02 (0.31), residues: 283 loop : 0.23 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 372 TYR 0.013 0.001 TYR D 294 PHE 0.021 0.001 PHE A 223 TRP 0.035 0.002 TRP A 86 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00332 (12024) covalent geometry : angle 0.61657 (16320) hydrogen bonds : bond 0.03096 ( 466) hydrogen bonds : angle 4.47437 ( 1230) link_TRANS : bond 0.00130 ( 8) link_TRANS : angle 0.31677 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 104 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8497 (tt) REVERT: A 190 MET cc_start: 0.6931 (tpp) cc_final: 0.6536 (tpp) REVERT: A 207 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6784 (tm-30) REVERT: A 353 GLN cc_start: 0.8045 (mm110) cc_final: 0.7669 (tm-30) REVERT: B 16 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7727 (ptp) REVERT: B 132 MET cc_start: 0.7646 (tpp) cc_final: 0.7294 (tpt) REVERT: B 153 MET cc_start: 0.7625 (tmm) cc_final: 0.7202 (tmt) REVERT: B 259 GLU cc_start: 0.7831 (tp30) cc_final: 0.7492 (tp30) REVERT: B 328 LYS cc_start: 0.8044 (tptt) cc_final: 0.7832 (tttp) REVERT: C 68 LYS cc_start: 0.8648 (ptmm) cc_final: 0.8348 (pttp) REVERT: D 151 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7835 (pt) REVERT: D 256 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7816 (ttt180) REVERT: D 294 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6175 (t80) outliers start: 54 outliers final: 44 residues processed: 170 average time/residue: 0.0880 time to fit residues: 23.3478 Evaluate side-chains 171 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 102 optimal weight: 0.8980 chunk 74 optimal weight: 0.0570 chunk 73 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 80 optimal weight: 0.4980 chunk 122 optimal weight: 0.0970 chunk 133 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 371 HIS D 252 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.129648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112891 restraints weight = 18424.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115961 restraints weight = 11409.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118164 restraints weight = 7949.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119689 restraints weight = 5964.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120855 restraints weight = 4771.257| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12032 Z= 0.110 Angle : 0.599 11.539 16344 Z= 0.276 Chirality : 0.044 0.233 1816 Planarity : 0.004 0.042 2064 Dihedral : 7.543 107.212 1708 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.47 % Allowed : 23.23 % Favored : 73.31 % 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 aren not related in a simple way. whole: 0.32 (0.23), residues: 1439 helix: 0.93 (0.23), residues: 557 sheet: -0.93 (0.31), residues: 283 loop : 0.33 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 372 TYR 0.014 0.001 TYR D 294 PHE 0.016 0.001 PHE A 223 TRP 0.033 0.001 TRP A 86 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00261 (12024) covalent geometry : angle 0.59959 (16320) hydrogen bonds : bond 0.02750 ( 466) hydrogen bonds : angle 4.39246 ( 1230) link_TRANS : bond 0.00100 ( 8) link_TRANS : angle 0.30387 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1822.45 seconds wall clock time: 32 minutes 38.14 seconds (1958.14 seconds total)