Starting phenix.real_space_refine on Sun May 3 07:48:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjm_50506/05_2026/9fjm_50506.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjm_50506/05_2026/9fjm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fjm_50506/05_2026/9fjm_50506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjm_50506/05_2026/9fjm_50506.map" model { file = "/net/cci-nas-00/data/ceres_data/9fjm_50506/05_2026/9fjm_50506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjm_50506/05_2026/9fjm_50506.cif" } 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-2.1rc2-6044/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: 3.03, per 1000 atoms: 0.26 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: 1.20 Conformation dependent library (CDL) restraints added in 555.1 milliseconds 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: 2.06 Time building geometry restraints manager: 1.45 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=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.525 1.571 -0.046 2.10e-02 2.27e+03 4.71e+00 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.525 1.570 -0.045 2.10e-02 2.27e+03 4.58e+00 bond pdb=" CA EEP I 2 " pdb=" C EEP I 2 " ideal model delta sigma weight residual 1.525 1.570 -0.045 2.10e-02 2.27e+03 4.53e+00 bond pdb=" CA EEP K 2 " pdb=" C EEP K 2 " ideal model delta sigma weight residual 1.525 1.570 -0.045 2.10e-02 2.27e+03 4.50e+00 bond pdb=" C EEP I 2 " pdb=" O EEP I 2 " ideal model delta sigma weight residual 1.231 1.263 -0.032 2.00e-02 2.50e+03 2.52e+00 ... (remaining 12019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 16025 1.85 - 3.70: 227 3.70 - 5.55: 49 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=" C EEP H 2 " pdb=" CA EEP H 2 " pdb=" CB EEP H 2 " ideal model delta sigma weight residual 110.50 106.34 4.16 1.50e+00 4.44e-01 7.70e+00 angle pdb=" C EEP I 2 " pdb=" CA EEP I 2 " pdb=" CB EEP I 2 " ideal model delta sigma weight residual 110.50 106.50 4.00 1.50e+00 4.44e-01 7.10e+00 angle pdb=" C EEP J 2 " pdb=" CA EEP J 2 " pdb=" CB EEP J 2 " ideal model delta sigma weight residual 110.50 106.56 3.94 1.50e+00 4.44e-01 6.91e+00 ... (remaining 16315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.20: 6398 20.20 - 40.40: 678 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: 1266 0.037 - 0.074: 383 0.074 - 0.110: 144 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: 10.350 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.560 Find NCS groups from input model: 0.250 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:1.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.230 ------------------------------------------------------------------------------- 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 : 0.003 0.046 12032 Z= 0.116 Angle : 0.601 16.244 16344 Z= 0.286 Chirality : 0.042 0.184 1816 Planarity : 0.004 0.051 2064 Dihedral : 16.705 100.999 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 are 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 0.00257 (12024) covalent geometry : angle 0.58010 (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 : 0.459 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: 0.0828 time to fit residues: 18.1635 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 : 0.420 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.123734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106340 restraints weight = 18797.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109277 restraints weight = 11995.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111405 restraints weight = 8527.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112971 restraints weight = 6504.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.114053 restraints weight = 5233.286| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12032 Z= 0.248 Angle : 0.690 7.644 16344 Z= 0.334 Chirality : 0.049 0.233 1816 Planarity : 0.005 0.054 2064 Dihedral : 7.910 112.978 1709 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.00 % Allowed : 19.60 % 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 are not related in a simple way. whole: -0.35 (0.22), residues: 1439 helix: -0.19 (0.21), residues: 567 sheet: -0.72 (0.33), residues: 242 loop : 0.19 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 372 TYR 0.015 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 B 101 Details of bonding type rmsd covalent geometry : bond 0.00591 (12024) covalent geometry : angle 0.69019 (16320) hydrogen bonds : bond 0.05851 ( 466) hydrogen bonds : angle 5.51656 ( 1230) link_TRANS : bond 0.00270 ( 8) link_TRANS : angle 0.62632 ( 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 202 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 140 time to evaluate : 0.426 Fit side-chains REVERT: C 283 MET cc_start: 0.8311 (tpp) cc_final: 0.6983 (mpp) REVERT: C 292 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7597 (t0) REVERT: D 9 VAL cc_start: 0.9027 (t) cc_final: 0.8744 (m) REVERT: D 294 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7892 (t80) outliers start: 62 outliers final: 40 residues processed: 180 average time/residue: 0.0782 time to fit residues: 22.2784 Evaluate side-chains 167 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 294 TYR 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: 1.9990 chunk 7 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 138 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 C 12 ASN D 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.108074 restraints weight = 18670.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.111211 restraints weight = 11591.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113472 restraints weight = 8070.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115056 restraints weight = 6058.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116279 restraints weight = 4838.020| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1592 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= 0.142 Angle : 0.598 8.062 16344 Z= 0.282 Chirality : 0.045 0.209 1816 Planarity : 0.004 0.050 2064 Dihedral : 7.693 111.134 1708 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.19 % Allowed : 20.08 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.23), residues: 1439 helix: 0.18 (0.22), residues: 570 sheet: -0.82 (0.32), residues: 258 loop : 0.37 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.011 0.001 TYR C 362 PHE 0.012 0.001 PHE A 223 TRP 0.009 0.001 TRP A 340 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00338 (12024) covalent geometry : angle 0.59831 (16320) hydrogen bonds : bond 0.04070 ( 466) hydrogen bonds : angle 5.01538 ( 1230) link_TRANS : bond 0.00098 ( 8) link_TRANS : angle 0.26481 ( 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 191 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 139 time to evaluate : 0.469 Fit side-chains REVERT: A 123 MET cc_start: 0.7795 (mtp) cc_final: 0.7507 (mtp) REVERT: A 207 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6804 (tm-30) REVERT: B 153 MET cc_start: 0.7600 (tmm) cc_final: 0.7115 (tmt) REVERT: C 283 MET cc_start: 0.8313 (tpp) cc_final: 0.6961 (mpp) REVERT: D 9 VAL cc_start: 0.8986 (t) cc_final: 0.8725 (m) REVERT: D 107 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6294 (tm-30) REVERT: D 132 MET cc_start: 0.6606 (ttt) cc_final: 0.6369 (ttt) outliers start: 52 outliers final: 31 residues processed: 175 average time/residue: 0.0897 time to fit residues: 24.1238 Evaluate side-chains 153 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 162 THR 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 82 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 297 THR Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.126315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108024 restraints weight = 18668.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.111429 restraints weight = 11228.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113805 restraints weight = 7662.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115499 restraints weight = 5710.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116714 restraints weight = 4524.509| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1855 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= 0.166 Angle : 0.615 9.077 16344 Z= 0.289 Chirality : 0.046 0.218 1816 Planarity : 0.004 0.047 2064 Dihedral : 7.695 112.853 1708 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.00 % Allowed : 20.08 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.23), residues: 1439 helix: 0.37 (0.22), residues: 561 sheet: -0.83 (0.32), residues: 254 loop : 0.23 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 372 TYR 0.021 0.001 TYR D 294 PHE 0.020 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 0.00399 (12024) covalent geometry : angle 0.61569 (16320) hydrogen bonds : bond 0.03678 ( 466) hydrogen bonds : angle 4.79756 ( 1230) link_TRANS : bond 0.00133 ( 8) link_TRANS : angle 0.25194 ( 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 191 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 129 time to evaluate : 0.421 Fit side-chains REVERT: A 104 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8403 (tt) REVERT: A 190 MET cc_start: 0.7071 (tpp) cc_final: 0.6808 (tpp) REVERT: A 207 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6869 (tm-30) REVERT: A 353 GLN cc_start: 0.8218 (mm110) cc_final: 0.7621 (tm-30) REVERT: B 153 MET cc_start: 0.7611 (tmm) cc_final: 0.7152 (tmt) REVERT: B 167 GLU cc_start: 0.7864 (tp30) cc_final: 0.7663 (tp30) REVERT: B 259 GLU cc_start: 0.7845 (tp30) cc_final: 0.7432 (tp30) REVERT: B 328 LYS cc_start: 0.7961 (tptt) cc_final: 0.7711 (tttp) REVERT: D 9 VAL cc_start: 0.9014 (t) cc_final: 0.8756 (m) REVERT: D 151 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7843 (pt) REVERT: D 294 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.6473 (t80) outliers start: 62 outliers final: 47 residues processed: 174 average time/residue: 0.0808 time to fit residues: 22.1361 Evaluate side-chains 177 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 127 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 288 ASP 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 123 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 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 207 GLU Chi-restraints excluded: chain C residue 267 LEU 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 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 324 THR 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: 0.5980 chunk 1 optimal weight: 4.9990 chunk 144 optimal weight: 0.0980 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 89 optimal weight: 0.0870 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.128328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.110084 restraints weight = 18496.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.113567 restraints weight = 10999.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115996 restraints weight = 7438.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.117725 restraints weight = 5497.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118954 restraints weight = 4324.992| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12032 Z= 0.120 Angle : 0.581 9.265 16344 Z= 0.270 Chirality : 0.044 0.220 1816 Planarity : 0.004 0.044 2064 Dihedral : 7.561 110.390 1708 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.52 % Allowed : 20.89 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.23), residues: 1439 helix: 0.57 (0.23), residues: 558 sheet: -0.98 (0.31), residues: 272 loop : 0.34 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 372 TYR 0.014 0.001 TYR D 294 PHE 0.013 0.001 PHE A 223 TRP 0.016 0.001 TRP A 86 HIS 0.005 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00284 (12024) covalent geometry : angle 0.58094 (16320) hydrogen bonds : bond 0.03157 ( 466) hydrogen bonds : angle 4.60972 ( 1230) link_TRANS : bond 0.00119 ( 8) link_TRANS : angle 0.22271 ( 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 187 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 131 time to evaluate : 0.389 Fit side-chains REVERT: A 205 GLU cc_start: 0.6740 (mp0) cc_final: 0.6345 (pm20) REVERT: A 207 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6807 (tm-30) REVERT: A 353 GLN cc_start: 0.8204 (mm110) cc_final: 0.7660 (tm-30) REVERT: B 16 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7807 (ptp) REVERT: B 132 MET cc_start: 0.7671 (tpp) cc_final: 0.7197 (tpt) REVERT: B 153 MET cc_start: 0.7587 (tmm) cc_final: 0.7159 (tmt) REVERT: B 167 GLU cc_start: 0.7844 (tp30) cc_final: 0.7617 (tp30) REVERT: B 259 GLU cc_start: 0.7798 (tp30) cc_final: 0.7375 (tp30) REVERT: B 328 LYS cc_start: 0.7950 (tptt) cc_final: 0.7706 (tttp) REVERT: C 123 MET cc_start: 0.7144 (tpp) cc_final: 0.6849 (mmt) REVERT: C 125 GLU cc_start: 0.7244 (mm-30) cc_final: 0.7023 (mt-10) REVERT: D 9 VAL cc_start: 0.8980 (t) cc_final: 0.8741 (m) REVERT: D 107 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6305 (tm-30) REVERT: D 294 TYR cc_start: 0.7581 (OUTLIER) cc_final: 0.6339 (t80) outliers start: 56 outliers final: 41 residues processed: 175 average time/residue: 0.0814 time to fit residues: 22.5232 Evaluate side-chains 167 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain A residue 162 THR 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 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 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 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 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 318 THR 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: 0.8980 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.126696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109453 restraints weight = 18720.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112543 restraints weight = 11655.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114707 restraints weight = 8129.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.116272 restraints weight = 6155.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117416 restraints weight = 4920.944| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12032 Z= 0.161 Angle : 0.598 9.375 16344 Z= 0.280 Chirality : 0.045 0.230 1816 Planarity : 0.004 0.044 2064 Dihedral : 7.615 112.599 1708 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.00 % Allowed : 21.13 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.23), residues: 1439 helix: 0.60 (0.23), residues: 562 sheet: -0.96 (0.31), residues: 270 loop : 0.27 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 372 TYR 0.013 0.001 TYR D 294 PHE 0.019 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 0.00387 (12024) covalent geometry : angle 0.59812 (16320) hydrogen bonds : bond 0.03361 ( 466) hydrogen bonds : angle 4.60315 ( 1230) link_TRANS : bond 0.00122 ( 8) link_TRANS : angle 0.26526 ( 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 191 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 129 time to evaluate : 0.508 Fit side-chains REVERT: A 104 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8451 (tt) REVERT: A 207 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6784 (tm-30) REVERT: A 353 GLN cc_start: 0.8138 (mm110) cc_final: 0.7685 (tm-30) REVERT: B 16 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7781 (ptp) REVERT: B 132 MET cc_start: 0.7745 (tpp) cc_final: 0.7373 (tpt) REVERT: B 153 MET cc_start: 0.7586 (tmm) cc_final: 0.7116 (tmt) REVERT: B 328 LYS cc_start: 0.7965 (tptt) cc_final: 0.7743 (tttp) REVERT: C 125 GLU cc_start: 0.7249 (mm-30) cc_final: 0.7034 (mt-10) REVERT: D 9 VAL cc_start: 0.9025 (t) cc_final: 0.8753 (m) REVERT: D 256 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7804 (ttt180) REVERT: D 294 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.6331 (t80) outliers start: 62 outliers final: 47 residues processed: 177 average time/residue: 0.0849 time to fit residues: 23.4850 Evaluate side-chains 170 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 119 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 348 SER Chi-restraints excluded: chain D residue 349 LEU 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: 0.7980 chunk 130 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 123 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: 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 = 0.3625 r_free = 0.3625 target = 0.126719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109443 restraints weight = 18579.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.112565 restraints weight = 11651.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114765 restraints weight = 8132.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.116306 restraints weight = 6144.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117365 restraints weight = 4921.849| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12032 Z= 0.156 Angle : 0.614 10.475 16344 Z= 0.287 Chirality : 0.045 0.233 1816 Planarity : 0.004 0.044 2064 Dihedral : 7.631 112.473 1708 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.48 % Allowed : 21.53 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.23), residues: 1439 helix: 0.63 (0.23), residues: 562 sheet: -0.93 (0.31), residues: 276 loop : 0.25 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 372 TYR 0.012 0.001 TYR D 294 PHE 0.030 0.001 PHE A 223 TRP 0.020 0.001 TRP A 86 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00376 (12024) covalent geometry : angle 0.61483 (16320) hydrogen bonds : bond 0.03323 ( 466) hydrogen bonds : angle 4.59364 ( 1230) link_TRANS : bond 0.00122 ( 8) link_TRANS : angle 0.25555 ( 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 190 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 122 time to evaluate : 0.415 Fit side-chains REVERT: A 205 GLU cc_start: 0.6908 (mp0) cc_final: 0.6336 (pm20) REVERT: A 207 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6780 (tm-30) REVERT: A 353 GLN cc_start: 0.8124 (mm110) cc_final: 0.7700 (tm-30) REVERT: B 16 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7774 (ptp) REVERT: B 132 MET cc_start: 0.7754 (tpp) cc_final: 0.7458 (tpt) REVERT: B 153 MET cc_start: 0.7579 (tmm) cc_final: 0.7113 (tmt) REVERT: B 259 GLU cc_start: 0.7813 (tp30) cc_final: 0.7406 (tp30) REVERT: B 328 LYS cc_start: 0.7980 (tptt) cc_final: 0.7757 (tttp) REVERT: D 9 VAL cc_start: 0.9030 (t) cc_final: 0.8757 (m) REVERT: D 151 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7822 (pt) REVERT: D 256 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7817 (ttt180) REVERT: D 294 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.6251 (t80) outliers start: 68 outliers final: 50 residues processed: 176 average time/residue: 0.0828 time to fit residues: 22.6142 Evaluate side-chains 174 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 120 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 176 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 288 ASP 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 124 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.107868 restraints weight = 18710.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.111314 restraints weight = 11272.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.113725 restraints weight = 7679.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.115432 restraints weight = 5724.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116640 restraints weight = 4535.239| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12032 Z= 0.163 Angle : 0.619 9.623 16344 Z= 0.289 Chirality : 0.046 0.237 1816 Planarity : 0.004 0.044 2064 Dihedral : 7.643 112.940 1708 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.00 % Allowed : 21.21 % 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 are not related in a simple way. whole: 0.13 (0.23), residues: 1439 helix: 0.76 (0.23), residues: 549 sheet: -1.06 (0.30), residues: 288 loop : 0.28 (0.27), residues: 602 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 0.026 0.001 PHE A 223 TRP 0.019 0.001 TRP A 86 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00393 (12024) covalent geometry : angle 0.61938 (16320) hydrogen bonds : bond 0.03378 ( 466) hydrogen bonds : angle 4.57634 ( 1230) link_TRANS : bond 0.00127 ( 8) link_TRANS : angle 0.26519 ( 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 185 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 123 time to evaluate : 0.396 Fit side-chains REVERT: A 104 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8446 (tt) REVERT: A 205 GLU cc_start: 0.6887 (mp0) cc_final: 0.6359 (pm20) REVERT: A 207 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6747 (tm-30) REVERT: A 353 GLN cc_start: 0.8147 (mm110) cc_final: 0.7699 (tm-30) REVERT: B 16 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7792 (ptp) REVERT: B 132 MET cc_start: 0.7796 (tpp) cc_final: 0.7419 (tpt) REVERT: B 153 MET cc_start: 0.7629 (tmm) cc_final: 0.7151 (tmt) REVERT: B 259 GLU cc_start: 0.7897 (tp30) cc_final: 0.7471 (tp30) REVERT: B 328 LYS cc_start: 0.7995 (tptt) cc_final: 0.7768 (tttp) REVERT: D 151 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7857 (pt) REVERT: D 256 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7813 (ttt180) REVERT: D 294 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.6251 (t80) outliers start: 62 outliers final: 49 residues processed: 173 average time/residue: 0.0850 time to fit residues: 22.7683 Evaluate side-chains 173 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 119 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 278 THR Chi-restraints excluded: chain A residue 288 ASP 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 38 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 43 optimal weight: 0.0570 chunk 89 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** 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 = 0.3615 r_free = 0.3615 target = 0.125707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107927 restraints weight = 18420.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111208 restraints weight = 11211.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113545 restraints weight = 7717.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115195 restraints weight = 5756.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116385 restraints weight = 4561.223| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12032 Z= 0.197 Angle : 0.639 9.559 16344 Z= 0.301 Chirality : 0.047 0.243 1816 Planarity : 0.004 0.044 2064 Dihedral : 7.737 114.523 1708 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.48 % Allowed : 20.97 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.23), residues: 1439 helix: 0.56 (0.23), residues: 568 sheet: -1.12 (0.30), residues: 288 loop : 0.08 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 372 TYR 0.012 0.001 TYR C 362 PHE 0.027 0.002 PHE A 223 TRP 0.025 0.002 TRP A 86 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00477 (12024) covalent geometry : angle 0.63901 (16320) hydrogen bonds : bond 0.03606 ( 466) hydrogen bonds : angle 4.62517 ( 1230) link_TRANS : bond 0.00152 ( 8) link_TRANS : angle 0.28983 ( 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 195 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 127 time to evaluate : 0.476 Fit side-chains REVERT: A 104 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8451 (tt) REVERT: A 205 GLU cc_start: 0.6839 (mp0) cc_final: 0.6341 (pm20) REVERT: A 207 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6660 (tm-30) REVERT: A 353 GLN cc_start: 0.8128 (mm110) cc_final: 0.7691 (tm-30) REVERT: B 100 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6367 (pm20) REVERT: B 132 MET cc_start: 0.7825 (tpp) cc_final: 0.7435 (tpt) REVERT: B 153 MET cc_start: 0.7633 (tmm) cc_final: 0.7189 (tmt) REVERT: B 259 GLU cc_start: 0.7942 (tp30) cc_final: 0.7511 (tp30) REVERT: B 328 LYS cc_start: 0.7998 (tptt) cc_final: 0.7778 (tttp) REVERT: D 151 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7893 (pt) REVERT: D 256 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7845 (ttt180) REVERT: D 294 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6253 (t80) outliers start: 68 outliers final: 56 residues processed: 181 average time/residue: 0.0832 time to fit residues: 23.6683 Evaluate side-chains 183 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 122 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 120 THR Chi-restraints excluded: chain A residue 143 TYR 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 257 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 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 100 GLU 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 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 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 160 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 217 CYS 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 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 327 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 19 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN 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 = 0.3639 r_free = 0.3639 target = 0.127499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109411 restraints weight = 18566.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112804 restraints weight = 11203.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115208 restraints weight = 7635.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.116896 restraints weight = 5683.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118123 restraints weight = 4496.095| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12032 Z= 0.142 Angle : 0.617 9.916 16344 Z= 0.289 Chirality : 0.045 0.242 1816 Planarity : 0.004 0.044 2064 Dihedral : 7.643 112.085 1708 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.44 % Allowed : 22.50 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.23), residues: 1439 helix: 0.69 (0.23), residues: 562 sheet: -1.08 (0.30), residues: 290 loop : 0.12 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 372 TYR 0.014 0.001 TYR D 294 PHE 0.027 0.001 PHE A 223 TRP 0.027 0.002 TRP A 86 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00345 (12024) covalent geometry : angle 0.61740 (16320) hydrogen bonds : bond 0.03241 ( 466) hydrogen bonds : angle 4.52771 ( 1230) link_TRANS : bond 0.00110 ( 8) link_TRANS : angle 0.24894 ( 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 175 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 120 time to evaluate : 0.326 Fit side-chains REVERT: A 104 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8467 (tt) REVERT: A 205 GLU cc_start: 0.6777 (mp0) cc_final: 0.6315 (pm20) REVERT: A 207 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6662 (tm-30) REVERT: A 237 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6804 (mm-30) REVERT: A 353 GLN cc_start: 0.8064 (mm110) cc_final: 0.7633 (tm-30) REVERT: B 132 MET cc_start: 0.7772 (tpp) cc_final: 0.7331 (tpt) REVERT: B 153 MET cc_start: 0.7629 (tmm) cc_final: 0.7184 (tmt) REVERT: B 259 GLU cc_start: 0.7874 (tp30) cc_final: 0.7427 (tp30) REVERT: B 328 LYS cc_start: 0.7992 (tptt) cc_final: 0.7775 (tttp) REVERT: D 151 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7835 (pt) REVERT: D 294 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6205 (t80) outliers start: 55 outliers final: 45 residues processed: 165 average time/residue: 0.0827 time to fit residues: 21.5260 Evaluate side-chains 164 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 116 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 257 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR 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 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 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 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 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 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 327 ILE Chi-restraints excluded: chain D residue 349 LEU 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: 2.9990 chunk 73 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 80 optimal weight: 0.0470 chunk 122 optimal weight: 0.9980 chunk 133 optimal weight: 0.0050 chunk 144 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.4892 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.127379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.109267 restraints weight = 18489.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112621 restraints weight = 11216.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.114993 restraints weight = 7671.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116685 restraints weight = 5730.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117932 restraints weight = 4533.402| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 12032 Z= 0.180 Angle : 0.862 59.198 16344 Z= 0.479 Chirality : 0.052 1.139 1816 Planarity : 0.004 0.044 2064 Dihedral : 7.684 112.086 1708 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.11 % Allowed : 22.74 % Favored : 73.15 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.23), residues: 1439 helix: 0.70 (0.23), residues: 562 sheet: -1.11 (0.30), residues: 290 loop : 0.12 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 372 TYR 0.014 0.001 TYR D 294 PHE 0.027 0.001 PHE A 223 TRP 0.023 0.001 TRP A 86 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00392 (12024) covalent geometry : angle 0.86267 (16320) hydrogen bonds : bond 0.03213 ( 466) hydrogen bonds : angle 4.52793 ( 1230) link_TRANS : bond 0.00102 ( 8) link_TRANS : angle 0.24585 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1768.33 seconds wall clock time: 31 minutes 33.27 seconds (1893.27 seconds total)