Starting phenix.real_space_refine on Tue Nov 18 22:53:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rtt_19496/11_2025/8rtt_19496.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rtt_19496/11_2025/8rtt_19496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rtt_19496/11_2025/8rtt_19496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rtt_19496/11_2025/8rtt_19496.map" model { file = "/net/cci-nas-00/data/ceres_data/8rtt_19496/11_2025/8rtt_19496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rtt_19496/11_2025/8rtt_19496.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 11 5.49 5 Mg 4 5.21 5 S 119 5.16 5 C 11460 2.51 5 N 3083 2.21 5 O 3478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18155 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" 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: "B" 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: "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: "E" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3173 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 13, 'TRANS': 375} Chain breaks: 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: "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: "F" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3150 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.58, per 1000 atoms: 0.25 Number of scatterers: 18155 At special positions: 0 Unit cell: (113.52, 130.24, 181.28, 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 119 16.00 P 11 15.00 Mg 4 11.99 O 3478 8.00 N 3083 7.00 C 11460 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 " Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 816.3 milliseconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 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 J 4 " Number of C-beta restraints generated: 4256 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 24 sheets defined 58.2% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.564A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.673A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 127 removed outlier: 3.873A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.535A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.509A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.849A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.547A pdb=" N PHE A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.830A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.165A 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 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.963A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.977A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.543A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.750A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 127 removed outlier: 4.025A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.568A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.732A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.979A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.616A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.562A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.559A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.765A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.006A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.502A 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 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.547A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 366 removed outlier: 3.619A pdb=" N SER B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.099A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.551A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.640A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.967A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.512A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.801A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.540A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 232 removed outlier: 3.683A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.716A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 4.524A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 286 through 296 removed outlier: 4.333A pdb=" N LYS C 291 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.860A 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 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.538A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.528A pdb=" N SER C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.105A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.779A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.715A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 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: 3.747A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.792A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.533A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.581A pdb=" N PHE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.835A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.025A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.591A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.652A 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: 3.574A pdb=" N LEU D 349 " --> pdb=" O ILE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 356 removed outlier: 3.500A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET D 355 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 366 removed outlier: 3.667A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.133A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 1011 through 1025 removed outlier: 3.649A pdb=" N ASN E1015 " --> pdb=" O SER E1011 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY E1025 " --> pdb=" O LEU E1021 " (cutoff:3.500A) Processing helix chain 'E' and resid 1025 through 1034 removed outlier: 3.802A pdb=" N GLU E1029 " --> pdb=" O GLY E1025 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU E1032 " --> pdb=" O ASP E1028 " (cutoff:3.500A) Processing helix chain 'E' and resid 1054 through 1065 removed outlier: 3.651A pdb=" N LYS E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) Processing helix chain 'E' and resid 1072 through 1082 Processing helix chain 'E' and resid 1084 through 1086 No H-bonds generated for 'chain 'E' and resid 1084 through 1086' Processing helix chain 'E' and resid 1087 through 1095 removed outlier: 3.911A pdb=" N GLU E1092 " --> pdb=" O ASN E1088 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE E1093 " --> pdb=" O GLU E1089 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E1094 " --> pdb=" O CYS E1090 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER E1095 " --> pdb=" O VAL E1091 " (cutoff:3.500A) Processing helix chain 'E' and resid 1096 through 1101 removed outlier: 3.527A pdb=" N LEU E1100 " --> pdb=" O SER E1096 " (cutoff:3.500A) Processing helix chain 'E' and resid 1102 through 1110 Processing helix chain 'E' and resid 1133 through 1143 Processing helix chain 'E' and resid 1149 through 1186 removed outlier: 3.501A pdb=" N THR E1165 " --> pdb=" O ASN E1161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR E1167 " --> pdb=" O ILE E1163 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLU E1168 " --> pdb=" O GLU E1164 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASN E1169 " --> pdb=" O THR E1165 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG E1172 " --> pdb=" O GLU E1168 " (cutoff:3.500A) Processing helix chain 'E' and resid 1187 through 1205 removed outlier: 3.554A pdb=" N LYS E1191 " --> pdb=" O SER E1187 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET E1204 " --> pdb=" O LEU E1200 " (cutoff:3.500A) Processing helix chain 'E' and resid 1206 through 1210 removed outlier: 3.908A pdb=" N GLN E1210 " --> pdb=" O TYR E1207 " (cutoff:3.500A) Processing helix chain 'E' and resid 1215 through 1222 removed outlier: 3.671A pdb=" N GLN E1220 " --> pdb=" O GLY E1217 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU E1222 " --> pdb=" O LEU E1219 " (cutoff:3.500A) Processing helix chain 'E' and resid 1233 through 1246 removed outlier: 3.837A pdb=" N ILE E1240 " --> pdb=" O HIS E1236 " (cutoff:3.500A) Processing helix chain 'E' and resid 1247 through 1250 Processing helix chain 'E' and resid 1257 through 1263 Processing helix chain 'E' and resid 1266 through 1291 removed outlier: 3.633A pdb=" N LEU E1277 " --> pdb=" O GLU E1273 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE E1278 " --> pdb=" O CYS E1274 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE E1286 " --> pdb=" O GLN E1282 " (cutoff:3.500A) Processing helix chain 'E' and resid 1292 through 1295 removed outlier: 3.532A pdb=" N ASP E1295 " --> pdb=" O ALA E1292 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1292 through 1295' Processing helix chain 'E' and resid 1304 through 1341 Proline residue: E1311 - end of helix removed outlier: 3.512A pdb=" N MET E1314 " --> pdb=" O LEU E1310 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU E1315 " --> pdb=" O PRO E1311 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE E1322 " --> pdb=" O LYS E1318 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE E1341 " --> pdb=" O ALA E1337 " (cutoff:3.500A) Processing helix chain 'E' and resid 1347 through 1353 Processing helix chain 'E' and resid 1354 through 1385 removed outlier: 3.623A pdb=" N VAL E1358 " --> pdb=" O PHE E1354 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU E1378 " --> pdb=" O LYS E1374 " (cutoff:3.500A) Processing helix chain 'F' and resid 1005 through 1009 Processing helix chain 'F' and resid 1011 through 1024 removed outlier: 3.556A pdb=" N ASN F1015 " --> pdb=" O SER F1011 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE F1017 " --> pdb=" O GLU F1013 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU F1018 " --> pdb=" O ALA F1014 " (cutoff:3.500A) Processing helix chain 'F' and resid 1026 through 1034 removed outlier: 3.592A pdb=" N ASP F1031 " --> pdb=" O LEU F1027 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU F1032 " --> pdb=" O ASP F1028 " (cutoff:3.500A) Processing helix chain 'F' and resid 1054 through 1065 removed outlier: 3.782A pdb=" N LYS F1059 " --> pdb=" O SER F1055 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU F1060 " --> pdb=" O GLU F1056 " (cutoff:3.500A) Processing helix chain 'F' and resid 1066 through 1069 removed outlier: 3.553A pdb=" N SER F1069 " --> pdb=" O HIS F1066 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1066 through 1069' Processing helix chain 'F' and resid 1072 through 1080 removed outlier: 3.561A pdb=" N ARG F1078 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE F1080 " --> pdb=" O ILE F1076 " (cutoff:3.500A) Processing helix chain 'F' and resid 1081 through 1083 No H-bonds generated for 'chain 'F' and resid 1081 through 1083' Processing helix chain 'F' and resid 1084 through 1088 removed outlier: 3.554A pdb=" N ASN F1088 " --> pdb=" O ASP F1085 " (cutoff:3.500A) Processing helix chain 'F' and resid 1089 through 1095 removed outlier: 3.986A pdb=" N PHE F1093 " --> pdb=" O GLU F1089 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU F1094 " --> pdb=" O CYS F1090 " (cutoff:3.500A) Processing helix chain 'F' and resid 1096 through 1101 Processing helix chain 'F' and resid 1102 through 1110 Processing helix chain 'F' and resid 1133 through 1143 removed outlier: 3.626A pdb=" N LEU F1138 " --> pdb=" O ARG F1134 " (cutoff:3.500A) Processing helix chain 'F' and resid 1149 through 1186 removed outlier: 3.634A pdb=" N ILE F1162 " --> pdb=" O LYS F1158 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR F1165 " --> pdb=" O ASN F1161 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU F1168 " --> pdb=" O GLU F1164 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN F1169 " --> pdb=" O THR F1165 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG F1172 " --> pdb=" O GLU F1168 " (cutoff:3.500A) Processing helix chain 'F' and resid 1187 through 1205 removed outlier: 3.762A pdb=" N MET F1204 " --> pdb=" O LEU F1200 " (cutoff:3.500A) Processing helix chain 'F' and resid 1206 through 1210 removed outlier: 3.822A pdb=" N GLN F1210 " --> pdb=" O TYR F1207 " (cutoff:3.500A) Processing helix chain 'F' and resid 1215 through 1222 removed outlier: 3.925A pdb=" N GLN F1220 " --> pdb=" O GLY F1217 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG F1221 " --> pdb=" O SER F1218 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F1222 " --> pdb=" O LEU F1219 " (cutoff:3.500A) Processing helix chain 'F' and resid 1233 through 1246 removed outlier: 3.667A pdb=" N ILE F1237 " --> pdb=" O SER F1233 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F1238 " --> pdb=" O LEU F1234 " (cutoff:3.500A) Processing helix chain 'F' and resid 1247 through 1250 Processing helix chain 'F' and resid 1257 through 1263 Processing helix chain 'F' and resid 1266 through 1290 removed outlier: 3.606A pdb=" N LEU F1277 " --> pdb=" O GLU F1273 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F1278 " --> pdb=" O CYS F1274 " (cutoff:3.500A) Processing helix chain 'F' and resid 1291 through 1295 Processing helix chain 'F' and resid 1304 through 1340 Proline residue: F1311 - end of helix removed outlier: 3.938A pdb=" N MET F1314 " --> pdb=" O LEU F1310 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU F1315 " --> pdb=" O PRO F1311 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS F1318 " --> pdb=" O MET F1314 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP F1321 " --> pdb=" O THR F1317 " (cutoff:3.500A) Processing helix chain 'F' and resid 1347 through 1353 Processing helix chain 'F' and resid 1354 through 1377 removed outlier: 3.676A pdb=" N VAL F1358 " --> pdb=" O PHE F1354 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.576A pdb=" N PHE A 31 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 4.168A 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 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.652A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.774A pdb=" N PHE B 31 " --> pdb=" O CYS B 17 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL B 9 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 4.028A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) 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 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.714A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (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: 3.674A pdb=" N PHE C 31 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 9 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.919A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) 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 removed outlier: 6.582A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 9 removed outlier: 6.722A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 3.636A 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: 3.709A 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: 3.530A pdb=" N LYS D 68 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.921A 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 176 through 178 removed outlier: 3.543A pdb=" N LEU D 176 " --> pdb=" O THR D 162 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N MET D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC6, first strand: chain 'F' and resid 1114 through 1115 removed outlier: 3.732A pdb=" N ASP F1121 " --> pdb=" O ASP F1115 " (cutoff:3.500A) 844 hydrogen bonds defined for protein. 2280 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: 3.34 Time building geometry restraints manager: 2.23 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: 5935 1.35 - 1.46: 4197 1.46 - 1.58: 8181 1.58 - 1.70: 18 1.70 - 1.82: 205 Bond restraints: 18536 Sorted by residual: bond pdb=" N HYP J 6 " pdb=" CD HYP J 6 " ideal model delta sigma weight residual 1.473 1.636 -0.163 1.40e-02 5.10e+03 1.35e+02 bond pdb=" N HYP H 6 " pdb=" CD HYP H 6 " ideal model delta sigma weight residual 1.473 1.636 -0.163 1.40e-02 5.10e+03 1.35e+02 bond pdb=" N HYP I 6 " pdb=" CD HYP I 6 " ideal model delta sigma weight residual 1.473 1.635 -0.162 1.40e-02 5.10e+03 1.34e+02 bond pdb=" CG HYP J 6 " pdb=" CD HYP J 6 " ideal model delta sigma weight residual 1.530 1.366 0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" CG HYP H 6 " pdb=" CD HYP H 6 " ideal model delta sigma weight residual 1.530 1.367 0.163 2.00e-02 2.50e+03 6.64e+01 ... (remaining 18531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 24732 1.85 - 3.69: 278 3.69 - 5.54: 71 5.54 - 7.38: 16 7.38 - 9.23: 4 Bond angle restraints: 25101 Sorted by residual: angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.87 -4.87 1.10e+00 8.26e-01 1.96e+01 angle pdb=" N HYP J 6 " pdb=" CA HYP J 6 " pdb=" CB HYP J 6 " ideal model delta sigma weight residual 103.00 107.66 -4.66 1.10e+00 8.26e-01 1.79e+01 angle pdb=" N HYP I 6 " pdb=" CA HYP I 6 " pdb=" CB HYP I 6 " ideal model delta sigma weight residual 103.00 107.51 -4.51 1.10e+00 8.26e-01 1.68e+01 angle pdb=" CB MET E1087 " pdb=" CG MET E1087 " pdb=" SD MET E1087 " ideal model delta sigma weight residual 112.70 121.93 -9.23 3.00e+00 1.11e-01 9.46e+00 angle pdb=" CA GLU E1273 " pdb=" CB GLU E1273 " pdb=" CG GLU E1273 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.15e+00 ... (remaining 25096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.03: 10808 34.03 - 68.06: 374 68.06 - 102.09: 23 102.09 - 136.11: 3 136.11 - 170.14: 2 Dihedral angle restraints: 11210 sinusoidal: 4601 harmonic: 6609 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 129.86 170.14 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.71 -163.71 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 164.64 135.36 1 2.00e+01 2.50e-03 4.11e+01 ... (remaining 11207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2445 0.059 - 0.117: 319 0.117 - 0.176: 7 0.176 - 0.235: 0 0.235 - 0.293: 3 Chirality restraints: 2774 Sorted by residual: 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 2.42 0.29 2.00e-01 2.50e+01 2.15e+00 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 2.43 0.28 2.00e-01 2.50e+01 2.01e+00 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 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 2771 not shown) Planarity restraints: 3211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N TRP J 1 " 0.036 2.00e-02 2.50e+03 6.18e-02 3.82e+01 pdb=" CA ALA J 7 " 0.030 2.00e-02 2.50e+03 pdb=" C ALA J 7 " -0.107 2.00e-02 2.50e+03 pdb=" O ALA J 7 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N TRP I 1 " -0.031 2.00e-02 2.50e+03 5.44e-02 2.95e+01 pdb=" CA ALA I 7 " -0.027 2.00e-02 2.50e+03 pdb=" C ALA I 7 " 0.094 2.00e-02 2.50e+03 pdb=" O ALA I 7 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N TRP H 1 " 0.016 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" CA ALA H 7 " 0.014 2.00e-02 2.50e+03 pdb=" C ALA H 7 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA H 7 " 0.018 2.00e-02 2.50e+03 ... (remaining 3208 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 27 2.37 - 3.00: 9403 3.00 - 3.64: 26465 3.64 - 4.27: 40145 4.27 - 4.90: 68350 Nonbonded interactions: 144390 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.740 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.757 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.802 3.620 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.966 2.170 nonbonded pdb="MG MG A 402 " pdb=" O2 PO4 A 403 " model vdw 1.979 2.170 ... (remaining 144385 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' and resid 6 through 402) selection = (chain 'B' and resid 6 through 402) selection = (chain 'C' and resid 6 through 402) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 984 through 1377) selection = (chain 'F' and (resid 984 through 1036 or resid 1050 through 1377)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.230 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.004 0.164 18542 Z= 0.238 Angle : 0.552 23.568 25119 Z= 0.270 Chirality : 0.040 0.293 2774 Planarity : 0.003 0.035 3205 Dihedral : 16.494 170.142 6936 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.20 % Allowed : 20.25 % Favored : 79.55 % 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: 0.18 (0.18), residues: 2228 helix: 0.27 (0.16), residues: 1100 sheet: 0.36 (0.37), residues: 232 loop : 0.09 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.005 0.001 TYR D 166 PHE 0.009 0.001 PHE F1004 TRP 0.013 0.001 TRP F 995 HIS 0.004 0.001 HIS F1236 Details of bonding type rmsd covalent geometry : bond 0.00415 (18536) covalent geometry : angle 0.52189 (25101) hydrogen bonds : bond 0.28442 ( 840) hydrogen bonds : angle 7.83750 ( 2280) link_TRANS : bond 0.00637 ( 6) link_TRANS : angle 6.77508 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 149 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 993 MET cc_start: 0.1064 (pmm) cc_final: 0.0560 (mpp) REVERT: F 1154 MET cc_start: 0.8247 (mmp) cc_final: 0.7754 (mmm) outliers start: 4 outliers final: 1 residues processed: 150 average time/residue: 0.1209 time to fit residues: 30.2333 Evaluate side-chains 146 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 995 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.137560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.101883 restraints weight = 31731.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.099869 restraints weight = 23105.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.101183 restraints weight = 19101.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.101643 restraints weight = 15344.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.101984 restraints weight = 12678.381| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18542 Z= 0.196 Angle : 0.588 6.821 25119 Z= 0.294 Chirality : 0.044 0.257 2774 Planarity : 0.004 0.035 3205 Dihedral : 8.502 179.191 2551 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.51 % Allowed : 17.54 % Favored : 79.96 % 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: 0.95 (0.18), residues: 2228 helix: 1.07 (0.16), residues: 1063 sheet: 0.32 (0.32), residues: 276 loop : 0.38 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.011 0.001 TYR A 143 PHE 0.012 0.001 PHE B 31 TRP 0.023 0.002 TRP I 1 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00452 (18536) covalent geometry : angle 0.58824 (25101) hydrogen bonds : bond 0.05482 ( 840) hydrogen bonds : angle 5.02761 ( 2280) link_TRANS : bond 0.00404 ( 6) link_TRANS : angle 0.71637 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 325 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6630 (mmp) REVERT: C 78 ASN cc_start: 0.7799 (t0) cc_final: 0.7079 (t0) REVERT: C 313 MET cc_start: 0.8464 (tpp) cc_final: 0.7593 (ttm) REVERT: D 153 MET cc_start: 0.7973 (tmm) cc_final: 0.7706 (tpt) REVERT: E 993 MET cc_start: 0.1195 (pmm) cc_final: 0.0708 (mpp) REVERT: E 1378 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: F 1161 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8202 (m-40) outliers start: 49 outliers final: 28 residues processed: 199 average time/residue: 0.1144 time to fit residues: 38.3752 Evaluate side-chains 170 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1171 VAL Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1286 ILE Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1161 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 191 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 180 optimal weight: 9.9990 chunk 5 optimal weight: 0.2980 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 12 ASN A 78 ASN D 111 ASN E1169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.138921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105274 restraints weight = 31544.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103819 restraints weight = 21327.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.104631 restraints weight = 17593.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.105269 restraints weight = 14992.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105430 restraints weight = 12707.433| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 18542 Z= 0.105 Angle : 0.512 6.837 25119 Z= 0.249 Chirality : 0.041 0.193 2774 Planarity : 0.003 0.033 3205 Dihedral : 7.979 168.242 2551 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.79 % Allowed : 19.53 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.18), residues: 2228 helix: 1.40 (0.17), residues: 1050 sheet: 0.42 (0.32), residues: 268 loop : 0.45 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1134 TYR 0.018 0.001 TYR A 240 PHE 0.011 0.001 PHE D 31 TRP 0.013 0.001 TRP C 356 HIS 0.004 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00230 (18536) covalent geometry : angle 0.51176 (25101) hydrogen bonds : bond 0.03903 ( 840) hydrogen bonds : angle 4.48565 ( 2280) link_TRANS : bond 0.00111 ( 6) link_TRANS : angle 0.32856 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: B 87 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.8081 (t70) REVERT: C 313 MET cc_start: 0.8273 (tpp) cc_final: 0.7388 (ttm) REVERT: D 115 ASN cc_start: 0.8515 (m-40) cc_final: 0.8302 (m-40) REVERT: D 153 MET cc_start: 0.7931 (tmm) cc_final: 0.7701 (tpt) REVERT: D 227 MET cc_start: 0.8072 (tpp) cc_final: 0.7851 (tpp) REVERT: E 993 MET cc_start: 0.1201 (pmm) cc_final: 0.0643 (mpp) REVERT: E 1378 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6945 (mt-10) outliers start: 35 outliers final: 15 residues processed: 183 average time/residue: 0.1146 time to fit residues: 35.2387 Evaluate side-chains 156 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1091 VAL Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1061 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 78 optimal weight: 0.0670 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 223 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN C 12 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1064 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 = 0.3890 r_free = 0.3890 target = 0.132970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.098429 restraints weight = 32181.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096604 restraints weight = 23936.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.097693 restraints weight = 19702.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098290 restraints weight = 15477.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.098354 restraints weight = 13990.068| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18542 Z= 0.193 Angle : 0.568 6.777 25119 Z= 0.276 Chirality : 0.043 0.215 2774 Planarity : 0.004 0.036 3205 Dihedral : 7.521 130.486 2551 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.45 % Allowed : 19.22 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.18), residues: 2228 helix: 1.32 (0.17), residues: 1059 sheet: 0.28 (0.32), residues: 268 loop : 0.27 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 372 TYR 0.011 0.001 TYR A 240 PHE 0.010 0.001 PHE D 31 TRP 0.016 0.001 TRP F1312 HIS 0.006 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00459 (18536) covalent geometry : angle 0.56786 (25101) hydrogen bonds : bond 0.04045 ( 840) hydrogen bonds : angle 4.42946 ( 2280) link_TRANS : bond 0.00311 ( 6) link_TRANS : angle 0.27471 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: B 87 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.8107 (t70) REVERT: C 313 MET cc_start: 0.8402 (tpp) cc_final: 0.7724 (ttm) REVERT: D 115 ASN cc_start: 0.8687 (m-40) cc_final: 0.8435 (m110) REVERT: D 153 MET cc_start: 0.8010 (tmm) cc_final: 0.7753 (tpt) REVERT: D 227 MET cc_start: 0.8258 (tpp) cc_final: 0.7888 (tpp) REVERT: E 1378 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6804 (mt-10) outliers start: 48 outliers final: 33 residues processed: 182 average time/residue: 0.1142 time to fit residues: 34.9036 Evaluate side-chains 168 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1091 VAL Chi-restraints excluded: chain E residue 1171 VAL Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1286 ILE Chi-restraints excluded: chain E residue 1308 VAL Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1061 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 167 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 chunk 190 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 201 optimal weight: 20.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 161 HIS B 246 GLN C 12 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1064 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 = 0.3863 r_free = 0.3863 target = 0.130957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.096389 restraints weight = 31906.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.093702 restraints weight = 23003.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.094246 restraints weight = 20738.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.095151 restraints weight = 16980.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.095336 restraints weight = 13882.204| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 18542 Z= 0.269 Angle : 0.630 7.317 25119 Z= 0.310 Chirality : 0.046 0.239 2774 Planarity : 0.004 0.039 3205 Dihedral : 7.589 146.099 2551 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.48 % Allowed : 19.12 % Favored : 77.40 % 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: 0.73 (0.18), residues: 2228 helix: 1.14 (0.16), residues: 1062 sheet: -0.03 (0.32), residues: 268 loop : -0.01 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 372 TYR 0.013 0.001 TYR A 240 PHE 0.013 0.002 PHE B 266 TRP 0.013 0.002 TRP F1312 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00642 (18536) covalent geometry : angle 0.62991 (25101) hydrogen bonds : bond 0.04337 ( 840) hydrogen bonds : angle 4.51311 ( 2280) link_TRANS : bond 0.00416 ( 6) link_TRANS : angle 0.40091 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 141 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8871 (mt) REVERT: B 47 MET cc_start: 0.7163 (tpp) cc_final: 0.6877 (tpt) REVERT: B 87 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.8163 (t70) REVERT: C 176 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8792 (mp) REVERT: C 313 MET cc_start: 0.8485 (tpp) cc_final: 0.8140 (ttm) REVERT: D 115 ASN cc_start: 0.8668 (m-40) cc_final: 0.8189 (t0) REVERT: E 1194 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8737 (mm) REVERT: E 1378 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6652 (mt-10) outliers start: 68 outliers final: 46 residues processed: 198 average time/residue: 0.1072 time to fit residues: 36.1486 Evaluate side-chains 182 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 131 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1091 VAL Chi-restraints excluded: chain E residue 1170 LEU Chi-restraints excluded: chain E residue 1171 VAL Chi-restraints excluded: chain E residue 1194 LEU Chi-restraints excluded: chain E residue 1237 ILE Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1286 ILE Chi-restraints excluded: chain E residue 1308 VAL Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1061 PHE Chi-restraints excluded: chain F residue 1189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 159 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 210 optimal weight: 40.0000 chunk 0 optimal weight: 0.6980 chunk 221 optimal weight: 40.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN C 12 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1064 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 = 0.3878 r_free = 0.3878 target = 0.131957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097300 restraints weight = 31821.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.095788 restraints weight = 22486.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.096971 restraints weight = 18693.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.097538 restraints weight = 14371.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.097925 restraints weight = 12205.985| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 18542 Z= 0.239 Angle : 0.607 10.733 25119 Z= 0.294 Chirality : 0.045 0.245 2774 Planarity : 0.004 0.039 3205 Dihedral : 7.515 144.978 2551 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.32 % Allowed : 20.25 % Favored : 76.43 % 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: 0.69 (0.18), residues: 2228 helix: 1.16 (0.17), residues: 1062 sheet: -0.17 (0.32), residues: 264 loop : -0.05 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.012 0.001 TYR A 240 PHE 0.012 0.001 PHE B 31 TRP 0.011 0.001 TRP C 340 HIS 0.005 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00570 (18536) covalent geometry : angle 0.60738 (25101) hydrogen bonds : bond 0.04009 ( 840) hydrogen bonds : angle 4.43448 ( 2280) link_TRANS : bond 0.00388 ( 6) link_TRANS : angle 0.39073 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 139 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: B 47 MET cc_start: 0.7203 (tpp) cc_final: 0.6974 (tpt) REVERT: B 87 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.8108 (t70) REVERT: C 78 ASN cc_start: 0.7681 (t0) cc_final: 0.7370 (m-40) REVERT: C 313 MET cc_start: 0.8481 (tpp) cc_final: 0.8135 (ttm) REVERT: D 115 ASN cc_start: 0.8549 (m-40) cc_final: 0.8130 (t0) REVERT: D 227 MET cc_start: 0.8115 (tpp) cc_final: 0.7755 (tpp) REVERT: E 1194 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8796 (mm) REVERT: E 1378 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: F 1154 MET cc_start: 0.7976 (mmp) cc_final: 0.7730 (mmm) outliers start: 65 outliers final: 48 residues processed: 193 average time/residue: 0.1123 time to fit residues: 36.5044 Evaluate side-chains 183 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1091 VAL Chi-restraints excluded: chain E residue 1170 LEU Chi-restraints excluded: chain E residue 1171 VAL Chi-restraints excluded: chain E residue 1194 LEU Chi-restraints excluded: chain E residue 1237 ILE Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1286 ILE Chi-restraints excluded: chain E residue 1308 VAL Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 174 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 199 optimal weight: 30.0000 chunk 191 optimal weight: 9.9990 chunk 212 optimal weight: 30.0000 chunk 69 optimal weight: 0.4980 chunk 213 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.132894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.098178 restraints weight = 31832.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096737 restraints weight = 21171.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.097816 restraints weight = 18342.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.098414 restraints weight = 14196.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.098694 restraints weight = 12111.864| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18542 Z= 0.165 Angle : 0.563 12.155 25119 Z= 0.271 Chirality : 0.043 0.241 2774 Planarity : 0.004 0.038 3205 Dihedral : 7.304 141.752 2551 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.71 % Allowed : 20.91 % Favored : 76.38 % 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: 0.85 (0.18), residues: 2228 helix: 1.29 (0.17), residues: 1062 sheet: -0.05 (0.33), residues: 256 loop : 0.01 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F1172 TYR 0.011 0.001 TYR A 240 PHE 0.032 0.001 PHE F1190 TRP 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00392 (18536) covalent geometry : angle 0.56341 (25101) hydrogen bonds : bond 0.03513 ( 840) hydrogen bonds : angle 4.29631 ( 2280) link_TRANS : bond 0.00281 ( 6) link_TRANS : angle 0.32332 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 143 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8836 (mt) REVERT: A 330 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8917 (mp) REVERT: B 47 MET cc_start: 0.7247 (tpp) cc_final: 0.7016 (tpt) REVERT: B 87 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.8068 (t70) REVERT: C 78 ASN cc_start: 0.7578 (t0) cc_final: 0.7294 (m-40) REVERT: C 313 MET cc_start: 0.8398 (tpp) cc_final: 0.7800 (ttm) REVERT: D 115 ASN cc_start: 0.8602 (m-40) cc_final: 0.8141 (t0) REVERT: D 227 MET cc_start: 0.8080 (tpp) cc_final: 0.7789 (tpp) REVERT: E 1378 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6735 (mt-10) outliers start: 53 outliers final: 40 residues processed: 186 average time/residue: 0.1137 time to fit residues: 35.5104 Evaluate side-chains 181 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1091 VAL Chi-restraints excluded: chain E residue 1170 LEU Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1189 VAL Chi-restraints excluded: chain F residue 1326 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 76 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 147 optimal weight: 0.0170 chunk 198 optimal weight: 20.0000 chunk 169 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN C 12 ASN ** C 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 = 0.3917 r_free = 0.3917 target = 0.134754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.100399 restraints weight = 31736.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.098620 restraints weight = 20901.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.099220 restraints weight = 18932.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.100130 restraints weight = 15651.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.100215 restraints weight = 12690.090| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18542 Z= 0.105 Angle : 0.527 10.271 25119 Z= 0.253 Chirality : 0.041 0.230 2774 Planarity : 0.003 0.036 3205 Dihedral : 6.924 133.541 2551 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.99 % Allowed : 21.42 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.18), residues: 2228 helix: 1.47 (0.17), residues: 1062 sheet: -0.00 (0.32), residues: 268 loop : 0.12 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.010 0.001 TYR A 240 PHE 0.028 0.001 PHE F1190 TRP 0.030 0.001 TRP F1116 HIS 0.003 0.001 HIS F1066 Details of bonding type rmsd covalent geometry : bond 0.00242 (18536) covalent geometry : angle 0.52751 (25101) hydrogen bonds : bond 0.02989 ( 840) hydrogen bonds : angle 4.14851 ( 2280) link_TRANS : bond 0.00153 ( 6) link_TRANS : angle 0.22838 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8720 (mt) REVERT: A 237 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7481 (mm-30) REVERT: B 47 MET cc_start: 0.7313 (tpp) cc_final: 0.7073 (tpt) REVERT: B 87 HIS cc_start: 0.8362 (OUTLIER) cc_final: 0.8023 (t70) REVERT: C 78 ASN cc_start: 0.7420 (t0) cc_final: 0.7181 (m-40) REVERT: C 313 MET cc_start: 0.8337 (tpp) cc_final: 0.7578 (ttm) REVERT: D 115 ASN cc_start: 0.8642 (m-40) cc_final: 0.8082 (t0) REVERT: D 153 MET cc_start: 0.7957 (tmm) cc_final: 0.7595 (tpt) REVERT: D 227 MET cc_start: 0.8125 (tpp) cc_final: 0.7812 (tpp) REVERT: E 1194 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8688 (mm) REVERT: E 1378 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6861 (mt-10) REVERT: F 1154 MET cc_start: 0.8018 (mmp) cc_final: 0.7730 (mmm) outliers start: 39 outliers final: 29 residues processed: 179 average time/residue: 0.1168 time to fit residues: 35.3064 Evaluate side-chains 172 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1091 VAL Chi-restraints excluded: chain E residue 1194 LEU Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 87 optimal weight: 0.4980 chunk 166 optimal weight: 2.9990 chunk 207 optimal weight: 30.0000 chunk 100 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN C 12 ASN ** F1064 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 = 0.3894 r_free = 0.3894 target = 0.133057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.098326 restraints weight = 31581.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.096679 restraints weight = 21182.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.097841 restraints weight = 19125.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.098381 restraints weight = 15088.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.098625 restraints weight = 12100.814| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18542 Z= 0.171 Angle : 0.556 9.115 25119 Z= 0.268 Chirality : 0.043 0.241 2774 Planarity : 0.004 0.038 3205 Dihedral : 6.849 130.023 2551 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.15 % Allowed : 21.32 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.18), residues: 2228 helix: 1.43 (0.17), residues: 1062 sheet: 0.02 (0.33), residues: 256 loop : 0.10 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.010 0.001 TYR A 240 PHE 0.026 0.001 PHE F1190 TRP 0.017 0.001 TRP F1116 HIS 0.004 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00406 (18536) covalent geometry : angle 0.55647 (25101) hydrogen bonds : bond 0.03379 ( 840) hydrogen bonds : angle 4.20380 ( 2280) link_TRANS : bond 0.00264 ( 6) link_TRANS : angle 0.25092 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8749 (mt) REVERT: B 47 MET cc_start: 0.7320 (tpp) cc_final: 0.7108 (tpt) REVERT: B 87 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.8059 (t70) REVERT: C 78 ASN cc_start: 0.7607 (t0) cc_final: 0.7340 (m-40) REVERT: C 313 MET cc_start: 0.8420 (tpp) cc_final: 0.7638 (ttm) REVERT: D 115 ASN cc_start: 0.8602 (m-40) cc_final: 0.8154 (t0) REVERT: D 153 MET cc_start: 0.8003 (tmm) cc_final: 0.7638 (tpt) REVERT: D 227 MET cc_start: 0.8117 (tpp) cc_final: 0.7789 (tpp) REVERT: D 305 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7580 (ttm) REVERT: E 1194 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8726 (mm) REVERT: E 1378 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6806 (mt-10) REVERT: F 1154 MET cc_start: 0.7963 (mmp) cc_final: 0.7695 (mmm) outliers start: 42 outliers final: 33 residues processed: 176 average time/residue: 0.1142 time to fit residues: 33.5450 Evaluate side-chains 178 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1060 LEU Chi-restraints excluded: chain E residue 1091 VAL Chi-restraints excluded: chain E residue 1194 LEU Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 121 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 210 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 chunk 148 optimal weight: 40.0000 chunk 200 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN C 12 ASN ** F1064 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 = 0.3901 r_free = 0.3901 target = 0.133574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.098814 restraints weight = 31719.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.097251 restraints weight = 21121.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098374 restraints weight = 18594.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099005 restraints weight = 14708.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.099153 restraints weight = 11907.498| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 18542 Z= 0.158 Angle : 0.725 59.155 25119 Z= 0.398 Chirality : 0.043 0.505 2774 Planarity : 0.004 0.067 3205 Dihedral : 6.878 130.039 2551 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.15 % Allowed : 21.27 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.18), residues: 2228 helix: 1.45 (0.17), residues: 1062 sheet: -0.08 (0.33), residues: 256 loop : 0.10 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.009 0.001 TYR A 240 PHE 0.024 0.001 PHE F1190 TRP 0.016 0.001 TRP F1116 HIS 0.004 0.001 HIS E1066 Details of bonding type rmsd covalent geometry : bond 0.00356 (18536) covalent geometry : angle 0.72565 (25101) hydrogen bonds : bond 0.03301 ( 840) hydrogen bonds : angle 4.19879 ( 2280) link_TRANS : bond 0.00202 ( 6) link_TRANS : angle 0.24291 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8749 (mt) REVERT: B 47 MET cc_start: 0.7325 (tpp) cc_final: 0.7110 (tpt) REVERT: B 87 HIS cc_start: 0.8388 (OUTLIER) cc_final: 0.8053 (t70) REVERT: C 78 ASN cc_start: 0.7604 (t0) cc_final: 0.7334 (m-40) REVERT: C 313 MET cc_start: 0.8415 (tpp) cc_final: 0.7632 (ttm) REVERT: D 115 ASN cc_start: 0.8599 (m-40) cc_final: 0.8147 (t0) REVERT: D 153 MET cc_start: 0.7993 (tmm) cc_final: 0.7624 (tpt) REVERT: D 227 MET cc_start: 0.8119 (tpp) cc_final: 0.7789 (tpp) REVERT: D 305 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7587 (ttm) REVERT: E 1194 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8711 (mm) REVERT: E 1378 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: F 1154 MET cc_start: 0.7984 (mmp) cc_final: 0.7721 (mmm) outliers start: 42 outliers final: 34 residues processed: 176 average time/residue: 0.1176 time to fit residues: 34.6937 Evaluate side-chains 180 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1060 LEU Chi-restraints excluded: chain E residue 1091 VAL Chi-restraints excluded: chain E residue 1194 LEU Chi-restraints excluded: chain E residue 1237 ILE Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 34 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 162 optimal weight: 0.0670 chunk 115 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** F1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.133576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.099291 restraints weight = 31754.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096524 restraints weight = 22826.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.097755 restraints weight = 20085.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.098667 restraints weight = 15394.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.098842 restraints weight = 12791.176| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 18542 Z= 0.154 Angle : 0.723 58.465 25119 Z= 0.396 Chirality : 0.043 0.440 2774 Planarity : 0.004 0.067 3205 Dihedral : 6.876 130.039 2551 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.04 % Allowed : 21.42 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.18), residues: 2228 helix: 1.45 (0.17), residues: 1062 sheet: -0.08 (0.33), residues: 256 loop : 0.10 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.009 0.001 TYR A 240 PHE 0.023 0.001 PHE F1190 TRP 0.015 0.001 TRP F1116 HIS 0.004 0.001 HIS E1066 Details of bonding type rmsd covalent geometry : bond 0.00350 (18536) covalent geometry : angle 0.72284 (25101) hydrogen bonds : bond 0.03300 ( 840) hydrogen bonds : angle 4.19870 ( 2280) link_TRANS : bond 0.00203 ( 6) link_TRANS : angle 0.24260 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2614.50 seconds wall clock time: 46 minutes 11.52 seconds (2771.52 seconds total)