Starting phenix.real_space_refine on Tue Jun 10 15:03:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjm_50506/06_2025/9fjm_50506.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjm_50506/06_2025/9fjm_50506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fjm_50506/06_2025/9fjm_50506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjm_50506/06_2025/9fjm_50506.map" model { file = "/net/cci-nas-00/data/ceres_data/9fjm_50506/06_2025/9fjm_50506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjm_50506/06_2025/9fjm_50506.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7417 2.51 5 N 1975 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11772 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2803 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2847 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.06, per 1000 atoms: 0.85 Number of scatterers: 11772 At special positions: 0 Unit cell: (97.68, 80.08, 154.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 12 15.00 Mg 4 11.99 O 2280 8.00 N 1975 7.00 C 7417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " " TRP K 1 " - " ALA K 7 " " DTH K 4 " - " ALA K 3 " Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.6 seconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH K 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 24 sheets defined 49.7% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.596A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.736A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.621A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.614A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.618A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.614A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.708A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.635A pdb=" N MET A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.367A pdb=" N LYS A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.522A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.763A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 removed outlier: 3.648A pdb=" N ASP A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.708A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.715A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.696A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.034A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.504A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.729A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.989A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.585A pdb=" N MET B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.797A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Proline residue: B 258 - end of helix removed outlier: 4.755A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.533A pdb=" N TYR B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.533A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.552A pdb=" N ILE B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.636A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.985A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.546A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.544A pdb=" N LEU C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.829A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.971A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.658A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 4.063A pdb=" N ALA C 174 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 171 through 175' Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.535A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.652A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 232 removed outlier: 3.569A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.726A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.517A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.717A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 366 removed outlier: 3.784A pdb=" N SER C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.529A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.589A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.579A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.000A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.633A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.940A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.802A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.073A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.249A pdb=" N LYS D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.796A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.594A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.524A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 366 removed outlier: 3.527A pdb=" N ASP D 363 " --> pdb=" O LYS D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 4.363A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.585A pdb=" N PHE A 31 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 106 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.856A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.865A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 165 through 166 removed outlier: 3.907A pdb=" N TYR A 166 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.547A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.622A pdb=" N PHE B 31 " --> pdb=" O CYS B 17 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 133 " --> pdb=" O VAL B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.502A pdb=" N LEU B 176 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.685A pdb=" N TYR B 166 " --> pdb=" O TYR B 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.886A pdb=" N PHE C 31 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR C 106 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.530A pdb=" N ILE C 250 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 10 removed outlier: 3.819A pdb=" N THR D 106 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR D 133 " --> pdb=" O VAL D 103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 16 through 19 removed outlier: 3.812A pdb=" N PHE D 31 " --> pdb=" O CYS D 17 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.628A pdb=" N LYS D 68 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.637A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 176 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.637A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 removed outlier: 3.653A pdb=" N LYS D 238 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE D 250 " --> pdb=" O LYS D 238 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3806 1.35 - 1.46: 2759 1.46 - 1.58: 5303 1.58 - 1.70: 12 1.70 - 1.82: 144 Bond restraints: 12024 Sorted by residual: bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.00e+00 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.00e+00 bond pdb=" CB LYS B 291 " pdb=" CG LYS B 291 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.02e-01 ... (remaining 12019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 16032 1.85 - 3.70: 227 3.70 - 5.55: 42 5.55 - 7.40: 14 7.40 - 9.25: 5 Bond angle restraints: 16320 Sorted by residual: angle pdb=" CB MET A 355 " pdb=" CG MET A 355 " pdb=" SD MET A 355 " ideal model delta sigma weight residual 112.70 121.95 -9.25 3.00e+00 1.11e-01 9.51e+00 angle pdb=" CB LYS B 291 " pdb=" CG LYS B 291 " pdb=" CD LYS B 291 " ideal model delta sigma weight residual 111.30 118.00 -6.70 2.30e+00 1.89e-01 8.48e+00 angle pdb=" CA LEU A 242 " pdb=" CB LEU A 242 " pdb=" CG LEU A 242 " ideal model delta sigma weight residual 116.30 125.30 -9.00 3.50e+00 8.16e-02 6.62e+00 angle pdb=" CB MET D 325 " pdb=" CG MET D 325 " pdb=" SD MET D 325 " ideal model delta sigma weight residual 112.70 105.04 7.66 3.00e+00 1.11e-01 6.51e+00 angle pdb=" CB MET C 355 " pdb=" CG MET C 355 " pdb=" SD MET C 355 " ideal model delta sigma weight residual 112.70 120.27 -7.57 3.00e+00 1.11e-01 6.37e+00 ... (remaining 16315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.20: 6392 20.20 - 40.40: 684 40.40 - 60.60: 127 60.60 - 80.80: 29 80.80 - 101.00: 10 Dihedral angle restraints: 7242 sinusoidal: 2937 harmonic: 4305 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 41.00 -101.00 1 2.00e+01 2.50e-03 2.86e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 39.71 -99.71 1 2.00e+01 2.50e-03 2.80e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 8.07 -68.07 1 2.00e+01 2.50e-03 1.50e+01 ... (remaining 7239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1263 0.037 - 0.074: 382 0.074 - 0.110: 148 0.110 - 0.147: 18 0.147 - 0.184: 5 Chirality restraints: 1816 Sorted by residual: chirality pdb=" CA HYP H 6 " pdb=" N HYP H 6 " pdb=" C HYP H 6 " pdb=" CB HYP H 6 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA HYP I 6 " pdb=" N HYP I 6 " pdb=" C HYP I 6 " pdb=" CB HYP I 6 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CA HYP J 6 " pdb=" N HYP J 6 " pdb=" C HYP J 6 " pdb=" CB HYP J 6 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 1813 not shown) Planarity restraints: 2072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N TRP J 1 " -0.025 2.00e-02 2.50e+03 4.27e-02 1.83e+01 pdb=" CA ALA J 7 " -0.021 2.00e-02 2.50e+03 pdb=" C ALA J 7 " 0.074 2.00e-02 2.50e+03 pdb=" O ALA J 7 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 129 " 0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO C 130 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 130 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 130 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 257 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO D 258 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 258 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 258 " 0.025 5.00e-02 4.00e+02 ... (remaining 2069 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 37 2.39 - 3.02: 6454 3.02 - 3.65: 17430 3.65 - 4.27: 25917 4.27 - 4.90: 44047 Nonbonded interactions: 93885 Sorted by model distance: nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.766 3.620 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.782 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.785 3.620 nonbonded pdb=" CD1 TRP K 1 " pdb=" SG CYS K 5 " model vdw 1.808 3.620 nonbonded pdb="MG MG B 402 " pdb=" O2 PO4 B 403 " model vdw 2.050 2.170 ... (remaining 93880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 6 through 39 or resid 50 through 374 or resid 401 through \ 403)) selection = (chain 'C' and (resid 6 through 39 or resid 50 through 374 or resid 401 through \ 403)) selection = (chain 'D' and (resid 6 through 39 or resid 50 through 374 or resid 401 through \ 403)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 70.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.800 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12032 Z= 0.104 Angle : 0.594 16.244 16344 Z= 0.280 Chirality : 0.042 0.184 1816 Planarity : 0.004 0.051 2064 Dihedral : 16.752 100.999 4458 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.24 % Allowed : 22.26 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.23), residues: 1439 helix: -0.69 (0.22), residues: 521 sheet: -0.73 (0.39), residues: 193 loop : 0.58 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 86 HIS 0.003 0.001 HIS A 87 PHE 0.006 0.001 PHE B 223 TYR 0.012 0.001 TYR D 362 ARG 0.009 0.000 ARG B 372 Details of bonding type rmsd link_TRANS : bond 0.00468 ( 8) link_TRANS : angle 4.09484 ( 24) hydrogen bonds : bond 0.30713 ( 466) hydrogen bonds : angle 8.49159 ( 1230) covalent geometry : bond 0.00233 (12024) covalent geometry : angle 0.57368 (16320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 1.407 Fit side-chains revert: symmetry clash REVERT: D 132 MET cc_start: 0.6366 (ttt) cc_final: 0.6127 (ttt) REVERT: D 325 MET cc_start: 0.7436 (ttp) cc_final: 0.6949 (ttp) outliers start: 3 outliers final: 1 residues processed: 139 average time/residue: 0.2301 time to fit residues: 48.9053 Evaluate side-chains 131 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 12 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.124866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107511 restraints weight = 18617.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110464 restraints weight = 11817.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112596 restraints weight = 8371.543| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12032 Z= 0.222 Angle : 0.666 7.548 16344 Z= 0.323 Chirality : 0.048 0.225 1816 Planarity : 0.005 0.052 2064 Dihedral : 8.067 110.617 1709 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.44 % Allowed : 19.92 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.22), residues: 1439 helix: -0.04 (0.21), residues: 567 sheet: -0.65 (0.34), residues: 242 loop : 0.28 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 1 HIS 0.006 0.001 HIS B 101 PHE 0.012 0.002 PHE D 90 TYR 0.014 0.001 TYR C 362 ARG 0.004 0.000 ARG B 372 Details of bonding type rmsd link_TRANS : bond 0.00270 ( 8) link_TRANS : angle 0.53331 ( 24) hydrogen bonds : bond 0.05836 ( 466) hydrogen bonds : angle 5.51344 ( 1230) covalent geometry : bond 0.00526 (12024) covalent geometry : angle 0.66623 (16320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 139 time to evaluate : 1.444 Fit side-chains REVERT: C 283 MET cc_start: 0.8238 (tpp) cc_final: 0.6937 (mpp) REVERT: C 292 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7631 (t0) REVERT: D 9 VAL cc_start: 0.8993 (t) cc_final: 0.8731 (m) outliers start: 55 outliers final: 33 residues processed: 174 average time/residue: 0.2002 time to fit residues: 54.6718 Evaluate side-chains 161 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 18 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 96 optimal weight: 0.0470 chunk 41 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN B 101 HIS C 12 ASN D 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105979 restraints weight = 18629.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109271 restraints weight = 11327.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.111659 restraints weight = 7805.171| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12032 Z= 0.138 Angle : 0.603 8.219 16344 Z= 0.283 Chirality : 0.045 0.209 1816 Planarity : 0.004 0.049 2064 Dihedral : 7.928 110.427 1708 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.35 % Allowed : 20.08 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.23), residues: 1439 helix: 0.25 (0.22), residues: 563 sheet: -0.68 (0.33), residues: 250 loop : 0.30 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 1 HIS 0.007 0.001 HIS B 101 PHE 0.010 0.001 PHE A 223 TYR 0.013 0.001 TYR D 294 ARG 0.005 0.000 ARG B 372 Details of bonding type rmsd link_TRANS : bond 0.00133 ( 8) link_TRANS : angle 0.28606 ( 24) hydrogen bonds : bond 0.04116 ( 466) hydrogen bonds : angle 5.03708 ( 1230) covalent geometry : bond 0.00324 (12024) covalent geometry : angle 0.60349 (16320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 1.364 Fit side-chains REVERT: A 123 MET cc_start: 0.7857 (mtp) cc_final: 0.7539 (mtp) REVERT: A 202 THR cc_start: 0.7611 (t) cc_final: 0.7140 (p) REVERT: A 207 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6801 (tm-30) REVERT: B 153 MET cc_start: 0.7632 (tmm) cc_final: 0.7147 (tmt) REVERT: D 9 VAL cc_start: 0.8998 (t) cc_final: 0.8741 (m) REVERT: D 132 MET cc_start: 0.6616 (ttt) cc_final: 0.6379 (ttt) REVERT: D 294 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.6624 (t80) REVERT: D 346 LEU cc_start: 0.8663 (tp) cc_final: 0.8342 (tt) outliers start: 54 outliers final: 34 residues processed: 177 average time/residue: 0.2247 time to fit residues: 60.8592 Evaluate side-chains 162 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 35 optimal weight: 3.9990 chunk 140 optimal weight: 0.3980 chunk 124 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.126832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108704 restraints weight = 18437.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112070 restraints weight = 11030.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.114436 restraints weight = 7524.029| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12032 Z= 0.158 Angle : 0.604 8.991 16344 Z= 0.284 Chirality : 0.046 0.216 1816 Planarity : 0.004 0.046 2064 Dihedral : 7.899 111.861 1708 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.16 % Allowed : 19.60 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1439 helix: 0.40 (0.23), residues: 561 sheet: -0.82 (0.32), residues: 256 loop : 0.27 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 86 HIS 0.006 0.001 HIS B 101 PHE 0.020 0.001 PHE A 223 TYR 0.012 0.001 TYR D 294 ARG 0.006 0.000 ARG B 372 Details of bonding type rmsd link_TRANS : bond 0.00164 ( 8) link_TRANS : angle 0.26530 ( 24) hydrogen bonds : bond 0.03676 ( 466) hydrogen bonds : angle 4.78797 ( 1230) covalent geometry : bond 0.00377 (12024) covalent geometry : angle 0.60462 (16320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 137 time to evaluate : 1.415 Fit side-chains REVERT: A 104 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8436 (tt) REVERT: A 207 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6849 (tm-30) REVERT: A 353 GLN cc_start: 0.8250 (mm110) cc_final: 0.7597 (tm-30) REVERT: B 153 MET cc_start: 0.7630 (tmm) cc_final: 0.7111 (tmt) REVERT: B 259 GLU cc_start: 0.7827 (tp30) cc_final: 0.7409 (tp30) REVERT: B 328 LYS cc_start: 0.7947 (tptt) cc_final: 0.7685 (tttp) REVERT: D 9 VAL cc_start: 0.9029 (t) cc_final: 0.8774 (m) REVERT: D 294 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.6421 (t80) outliers start: 64 outliers final: 48 residues processed: 180 average time/residue: 0.2053 time to fit residues: 57.3108 Evaluate side-chains 177 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 127 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 37 optimal weight: 0.0870 chunk 21 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 112 optimal weight: 0.2980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 12 ASN D 12 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110292 restraints weight = 18382.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.113725 restraints weight = 10916.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116123 restraints weight = 7396.593| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12032 Z= 0.119 Angle : 0.580 9.361 16344 Z= 0.269 Chirality : 0.044 0.216 1816 Planarity : 0.004 0.044 2064 Dihedral : 7.758 109.798 1708 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.35 % Allowed : 20.48 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.23), residues: 1439 helix: 0.64 (0.23), residues: 554 sheet: -0.93 (0.31), residues: 272 loop : 0.40 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 86 HIS 0.007 0.001 HIS B 101 PHE 0.015 0.001 PHE A 223 TYR 0.013 0.001 TYR D 294 ARG 0.005 0.000 ARG B 372 Details of bonding type rmsd link_TRANS : bond 0.00130 ( 8) link_TRANS : angle 0.24281 ( 24) hydrogen bonds : bond 0.03141 ( 466) hydrogen bonds : angle 4.60342 ( 1230) covalent geometry : bond 0.00280 (12024) covalent geometry : angle 0.58042 (16320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 137 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: A 104 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8398 (tt) REVERT: A 190 MET cc_start: 0.7068 (tpp) cc_final: 0.6702 (tpp) REVERT: A 207 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6803 (tm-30) REVERT: A 259 GLU cc_start: 0.6948 (tp30) cc_final: 0.6708 (tp30) REVERT: A 353 GLN cc_start: 0.8231 (mm110) cc_final: 0.7656 (tm-30) REVERT: B 16 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7822 (ptp) REVERT: B 153 MET cc_start: 0.7582 (tmm) cc_final: 0.7122 (tmt) REVERT: B 259 GLU cc_start: 0.7802 (tp30) cc_final: 0.7394 (tp30) REVERT: B 328 LYS cc_start: 0.7973 (tptt) cc_final: 0.7715 (tttp) REVERT: C 125 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6993 (mt-10) REVERT: D 9 VAL cc_start: 0.8960 (t) cc_final: 0.8738 (m) REVERT: D 294 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.6399 (t80) outliers start: 54 outliers final: 37 residues processed: 175 average time/residue: 0.1900 time to fit residues: 51.7398 Evaluate side-chains 168 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 127 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 12 ASN D 12 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110880 restraints weight = 18689.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113980 restraints weight = 11587.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116190 restraints weight = 8049.756| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12032 Z= 0.132 Angle : 0.585 9.467 16344 Z= 0.271 Chirality : 0.045 0.222 1816 Planarity : 0.004 0.043 2064 Dihedral : 7.733 111.066 1708 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.44 % Allowed : 20.65 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1439 helix: 0.68 (0.23), residues: 561 sheet: -0.90 (0.31), residues: 267 loop : 0.36 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 86 HIS 0.004 0.001 HIS A 87 PHE 0.015 0.001 PHE A 223 TYR 0.012 0.001 TYR D 294 ARG 0.006 0.000 ARG B 372 Details of bonding type rmsd link_TRANS : bond 0.00123 ( 8) link_TRANS : angle 0.28786 ( 24) hydrogen bonds : bond 0.03129 ( 466) hydrogen bonds : angle 4.54418 ( 1230) covalent geometry : bond 0.00314 (12024) covalent geometry : angle 0.58507 (16320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 131 time to evaluate : 1.467 Fit side-chains REVERT: A 104 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8462 (tt) REVERT: A 207 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6757 (tm-30) REVERT: A 353 GLN cc_start: 0.8159 (mm110) cc_final: 0.7678 (tm-30) REVERT: B 16 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7798 (ptp) REVERT: B 153 MET cc_start: 0.7577 (tmm) cc_final: 0.7170 (tmt) REVERT: B 259 GLU cc_start: 0.7825 (tp30) cc_final: 0.7395 (tp30) REVERT: B 328 LYS cc_start: 0.7976 (tptt) cc_final: 0.7731 (tttp) REVERT: D 9 VAL cc_start: 0.8984 (t) cc_final: 0.8751 (m) REVERT: D 151 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7866 (pt) REVERT: D 294 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.6316 (t80) outliers start: 55 outliers final: 40 residues processed: 172 average time/residue: 0.1989 time to fit residues: 53.9409 Evaluate side-chains 170 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 0.0970 chunk 84 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.107606 restraints weight = 18641.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.110878 restraints weight = 11244.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113261 restraints weight = 7730.390| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12032 Z= 0.134 Angle : 0.588 9.557 16344 Z= 0.273 Chirality : 0.045 0.227 1816 Planarity : 0.004 0.042 2064 Dihedral : 7.703 111.499 1708 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 5.00 % Allowed : 20.65 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.23), residues: 1439 helix: 0.63 (0.23), residues: 569 sheet: -0.90 (0.31), residues: 267 loop : 0.40 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 86 HIS 0.004 0.001 HIS A 87 PHE 0.020 0.001 PHE A 223 TYR 0.013 0.001 TYR D 294 ARG 0.009 0.000 ARG B 372 Details of bonding type rmsd link_TRANS : bond 0.00123 ( 8) link_TRANS : angle 0.30668 ( 24) hydrogen bonds : bond 0.03114 ( 466) hydrogen bonds : angle 4.49130 ( 1230) covalent geometry : bond 0.00321 (12024) covalent geometry : angle 0.58785 (16320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 130 time to evaluate : 1.373 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6777 (tm-30) REVERT: A 353 GLN cc_start: 0.8157 (mm110) cc_final: 0.7668 (tm-30) REVERT: B 16 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7812 (ptp) REVERT: B 153 MET cc_start: 0.7608 (tmm) cc_final: 0.7195 (tmt) REVERT: B 167 GLU cc_start: 0.7778 (tp30) cc_final: 0.7522 (tp30) REVERT: B 259 GLU cc_start: 0.7862 (tp30) cc_final: 0.7467 (tp30) REVERT: B 328 LYS cc_start: 0.7993 (tptt) cc_final: 0.7739 (tttp) REVERT: D 151 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7843 (pt) REVERT: D 294 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.6261 (t80) outliers start: 62 outliers final: 45 residues processed: 176 average time/residue: 0.2081 time to fit residues: 55.9639 Evaluate side-chains 172 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 100 optimal weight: 2.9990 chunk 59 optimal weight: 0.0070 chunk 118 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.108704 restraints weight = 18478.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111910 restraints weight = 11410.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.114133 restraints weight = 7880.208| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12032 Z= 0.120 Angle : 0.589 9.827 16344 Z= 0.272 Chirality : 0.044 0.228 1816 Planarity : 0.004 0.043 2064 Dihedral : 7.618 110.703 1708 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.52 % Allowed : 21.77 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1439 helix: 0.70 (0.23), residues: 569 sheet: -0.87 (0.32), residues: 266 loop : 0.42 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 86 HIS 0.004 0.001 HIS A 87 PHE 0.018 0.001 PHE A 223 TYR 0.013 0.001 TYR D 294 ARG 0.008 0.000 ARG B 372 Details of bonding type rmsd link_TRANS : bond 0.00106 ( 8) link_TRANS : angle 0.30198 ( 24) hydrogen bonds : bond 0.02975 ( 466) hydrogen bonds : angle 4.43550 ( 1230) covalent geometry : bond 0.00287 (12024) covalent geometry : angle 0.58935 (16320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 128 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6790 (tm-30) REVERT: A 353 GLN cc_start: 0.8090 (mm110) cc_final: 0.7686 (tm-30) REVERT: B 16 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7800 (ptp) REVERT: B 153 MET cc_start: 0.7572 (tmm) cc_final: 0.7185 (tmt) REVERT: B 167 GLU cc_start: 0.7748 (tp30) cc_final: 0.7522 (tp30) REVERT: B 259 GLU cc_start: 0.7808 (tp30) cc_final: 0.7432 (tp30) REVERT: B 294 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: B 328 LYS cc_start: 0.8002 (tptt) cc_final: 0.7758 (tttp) REVERT: C 125 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6935 (mt-10) REVERT: D 151 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7826 (pt) REVERT: D 294 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.6162 (t80) outliers start: 56 outliers final: 43 residues processed: 169 average time/residue: 0.2222 time to fit residues: 57.7022 Evaluate side-chains 171 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 87 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 58 optimal weight: 0.0670 chunk 136 optimal weight: 0.6980 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.108124 restraints weight = 18502.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111167 restraints weight = 11608.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113314 restraints weight = 8131.762| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12032 Z= 0.145 Angle : 0.612 11.993 16344 Z= 0.283 Chirality : 0.045 0.232 1816 Planarity : 0.004 0.043 2064 Dihedral : 7.679 114.509 1708 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.27 % Allowed : 22.74 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.23), residues: 1439 helix: 0.74 (0.23), residues: 561 sheet: -0.90 (0.32), residues: 266 loop : 0.31 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 86 HIS 0.004 0.001 HIS A 87 PHE 0.018 0.001 PHE A 223 TYR 0.018 0.001 TYR B 294 ARG 0.009 0.000 ARG B 372 Details of bonding type rmsd link_TRANS : bond 0.00129 ( 8) link_TRANS : angle 0.33314 ( 24) hydrogen bonds : bond 0.03115 ( 466) hydrogen bonds : angle 4.45855 ( 1230) covalent geometry : bond 0.00350 (12024) covalent geometry : angle 0.61183 (16320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.7029 (tpp) cc_final: 0.6549 (tpp) REVERT: A 207 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6784 (tm-30) REVERT: A 353 GLN cc_start: 0.8121 (mm110) cc_final: 0.7673 (tm-30) REVERT: B 16 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7794 (ptp) REVERT: B 153 MET cc_start: 0.7593 (tmm) cc_final: 0.7172 (tmt) REVERT: B 259 GLU cc_start: 0.7787 (tp30) cc_final: 0.7440 (tp30) REVERT: B 291 LYS cc_start: 0.8160 (tppt) cc_final: 0.7831 (pttt) REVERT: B 328 LYS cc_start: 0.8071 (tptt) cc_final: 0.7846 (tttp) REVERT: C 125 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7124 (mt-10) REVERT: D 151 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7872 (pt) REVERT: D 294 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6189 (t80) outliers start: 53 outliers final: 40 residues processed: 164 average time/residue: 0.2386 time to fit residues: 61.5570 Evaluate side-chains 166 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 40 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 49 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.127319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109567 restraints weight = 18476.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112930 restraints weight = 11155.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.115291 restraints weight = 7602.916| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12032 Z= 0.145 Angle : 0.612 10.759 16344 Z= 0.284 Chirality : 0.045 0.235 1816 Planarity : 0.004 0.043 2064 Dihedral : 7.664 113.983 1708 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.11 % Allowed : 22.90 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.23), residues: 1439 helix: 0.78 (0.23), residues: 565 sheet: -0.95 (0.31), residues: 272 loop : 0.30 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 86 HIS 0.004 0.001 HIS A 87 PHE 0.018 0.001 PHE A 223 TYR 0.013 0.001 TYR D 294 ARG 0.009 0.000 ARG B 372 Details of bonding type rmsd link_TRANS : bond 0.00130 ( 8) link_TRANS : angle 0.33491 ( 24) hydrogen bonds : bond 0.03133 ( 466) hydrogen bonds : angle 4.44909 ( 1230) covalent geometry : bond 0.00350 (12024) covalent geometry : angle 0.61241 (16320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 129 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.7025 (tpp) cc_final: 0.6725 (tpp) REVERT: A 207 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6618 (tm-30) REVERT: A 353 GLN cc_start: 0.8037 (mm110) cc_final: 0.7605 (tm-30) REVERT: B 16 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7778 (ptp) REVERT: B 153 MET cc_start: 0.7608 (tmm) cc_final: 0.7171 (tmt) REVERT: B 259 GLU cc_start: 0.7827 (tp30) cc_final: 0.7470 (tp30) REVERT: B 291 LYS cc_start: 0.8151 (tppt) cc_final: 0.7810 (pttt) REVERT: C 82 MET cc_start: 0.8097 (tpt) cc_final: 0.7633 (tpt) REVERT: C 125 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7113 (mt-10) REVERT: D 107 GLU cc_start: 0.6627 (tp30) cc_final: 0.6301 (tm-30) REVERT: D 151 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7899 (pt) REVERT: D 256 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7828 (ttt180) REVERT: D 294 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.6257 (t80) REVERT: D 316 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7245 (mm-30) outliers start: 51 outliers final: 42 residues processed: 165 average time/residue: 0.2590 time to fit residues: 65.4200 Evaluate side-chains 170 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 25 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.126829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.109142 restraints weight = 18458.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112468 restraints weight = 11139.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.114842 restraints weight = 7612.955| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12032 Z= 0.151 Angle : 0.618 10.514 16344 Z= 0.288 Chirality : 0.045 0.237 1816 Planarity : 0.004 0.043 2064 Dihedral : 7.660 112.956 1708 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.35 % Allowed : 22.82 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), residues: 1439 helix: 0.84 (0.23), residues: 558 sheet: -1.07 (0.31), residues: 282 loop : 0.36 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 86 HIS 0.005 0.001 HIS A 87 PHE 0.019 0.001 PHE A 223 TYR 0.013 0.001 TYR D 294 ARG 0.009 0.000 ARG B 372 Details of bonding type rmsd link_TRANS : bond 0.00133 ( 8) link_TRANS : angle 0.35068 ( 24) hydrogen bonds : bond 0.03187 ( 466) hydrogen bonds : angle 4.44997 ( 1230) covalent geometry : bond 0.00367 (12024) covalent geometry : angle 0.61797 (16320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4502.25 seconds wall clock time: 83 minutes 29.82 seconds (5009.82 seconds total)