Starting phenix.real_space_refine on Wed Mar 4 15:33:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bt7_30171/03_2026/7bt7_30171.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bt7_30171/03_2026/7bt7_30171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bt7_30171/03_2026/7bt7_30171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bt7_30171/03_2026/7bt7_30171.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bt7_30171/03_2026/7bt7_30171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bt7_30171/03_2026/7bt7_30171.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9162 2.51 5 N 2463 2.21 5 O 2785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14530 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2875 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2881 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2878 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2873 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.57, per 1000 atoms: 0.25 Number of scatterers: 14530 At special positions: 0 Unit cell: (97.52, 91.16, 192.92, 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 105 16.00 P 10 15.00 Mg 5 11.99 O 2785 8.00 N 2463 7.00 C 9162 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 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 423.5 milliseconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 32 sheets defined 44.8% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.830A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.815A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.695A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.832A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.860A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.659A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 removed outlier: 4.195A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.814A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 removed outlier: 4.084A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.629A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 removed outlier: 4.286A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.595A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.537A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.522A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.798A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.512A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.788A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 removed outlier: 3.976A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.946A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.843A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 removed outlier: 4.198A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 284 removed outlier: 3.737A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 4.097A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.517A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 311 Processing helix chain 'B' and resid 312 through 319 Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.531A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 353 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 95 removed outlier: 3.627A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.503A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.758A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.917A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.950A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.587A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.887A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 removed outlier: 4.129A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.116A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 removed outlier: 3.712A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 354 removed outlier: 3.960A pdb=" N GLN C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.662A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.727A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 146 removed outlier: 3.568A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 4.102A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (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 217 removed outlier: 3.837A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 removed outlier: 4.144A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.598A pdb=" N GLY D 268 " --> pdb=" O SER D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.890A pdb=" N THR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 294 removed outlier: 4.313A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.076A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 319 removed outlier: 3.649A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.542A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.776A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.981A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 146 Processing helix chain 'E' and resid 181 through 197 removed outlier: 3.593A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.793A pdb=" N LYS E 215 " --> pdb=" O ASP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 230 Processing helix chain 'E' and resid 273 through 284 removed outlier: 3.583A pdb=" N THR E 278 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 removed outlier: 4.211A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 4.627A pdb=" N GLN E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.113A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.793A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.772A pdb=" N GLN A 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.732A pdb=" N ILE A 75 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 177 through 178 removed outlier: 3.689A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.587A pdb=" N LYS B 18 " --> pdb=" O ASP B 11 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.605A pdb=" N ILE B 75 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 239 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.569A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.663A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 removed outlier: 3.662A pdb=" N ILE C 75 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 150 through 151 Processing sheet with id=AB6, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.636A pdb=" N ASN C 162 " --> pdb=" O MET C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 239 through 241 Processing sheet with id=AB8, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.814A pdb=" N LYS D 18 " --> pdb=" O ASP D 11 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.645A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 71 through 72 removed outlier: 3.564A pdb=" N ILE D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AC3, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AC4, first strand: chain 'D' and resid 150 through 151 Processing sheet with id=AC5, first strand: chain 'D' and resid 160 through 162 removed outlier: 3.503A pdb=" N ASN D 162 " --> pdb=" O MET D 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 240 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.675A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS E 18 " --> pdb=" O ASP E 11 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 9 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.539A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 106 through 107 Processing sheet with id=AD2, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AD3, first strand: chain 'E' and resid 150 through 151 Processing sheet with id=AD4, first strand: chain 'E' and resid 154 through 155 removed outlier: 3.526A pdb=" N ASP E 154 " --> pdb=" O HIS E 161 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN E 162 " --> pdb=" O MET E 176 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 239 through 241 517 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4744 1.34 - 1.46: 3044 1.46 - 1.58: 6857 1.58 - 1.69: 15 1.69 - 1.81: 185 Bond restraints: 14845 Sorted by residual: bond pdb=" C MET B 305 " pdb=" N TYR B 306 " ideal model delta sigma weight residual 1.329 1.281 0.048 3.03e-02 1.09e+03 2.49e+00 bond pdb=" C CYS C 257 " pdb=" N PRO C 258 " ideal model delta sigma weight residual 1.336 1.350 -0.014 9.80e-03 1.04e+04 2.13e+00 bond pdb=" CA GLU A 99 " pdb=" C GLU A 99 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.80e-02 3.09e+03 1.97e+00 bond pdb=" C4 ADP D 402 " pdb=" C5 ADP D 402 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" C4 ADP B 402 " pdb=" C5 ADP B 402 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.38e+00 ... (remaining 14840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 19664 1.76 - 3.52: 394 3.52 - 5.29: 67 5.29 - 7.05: 19 7.05 - 8.81: 2 Bond angle restraints: 20146 Sorted by residual: angle pdb=" C GLY A 308 " pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta sigma weight residual 121.97 128.25 -6.28 1.80e+00 3.09e-01 1.22e+01 angle pdb=" C GLY B 308 " pdb=" N ILE B 309 " pdb=" CA ILE B 309 " ideal model delta sigma weight residual 121.97 127.61 -5.64 1.80e+00 3.09e-01 9.82e+00 angle pdb=" N PRO A 307 " pdb=" CA PRO A 307 " pdb=" C PRO A 307 " ideal model delta sigma weight residual 114.68 111.46 3.22 1.04e+00 9.25e-01 9.59e+00 angle pdb=" N ILE A 309 " pdb=" CA ILE A 309 " pdb=" C ILE A 309 " ideal model delta sigma weight residual 109.34 115.70 -6.36 2.08e+00 2.31e-01 9.35e+00 angle pdb=" N ILE D 250 " pdb=" CA ILE D 250 " pdb=" C ILE D 250 " ideal model delta sigma weight residual 106.21 109.20 -2.99 1.07e+00 8.73e-01 7.82e+00 ... (remaining 20141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.31: 8197 18.31 - 36.62: 605 36.62 - 54.92: 106 54.92 - 73.23: 23 73.23 - 91.54: 8 Dihedral angle restraints: 8939 sinusoidal: 3594 harmonic: 5345 Sorted by residual: dihedral pdb=" CA GLY A 308 " pdb=" C GLY A 308 " pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta harmonic sigma weight residual -180.00 -151.85 -28.15 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" C5' ADP A 402 " pdb=" O5' ADP A 402 " pdb=" PA ADP A 402 " pdb=" O2A ADP A 402 " ideal model delta sinusoidal sigma weight residual -60.00 31.54 -91.54 1 2.00e+01 2.50e-03 2.46e+01 dihedral pdb=" C5' ADP C 402 " pdb=" O5' ADP C 402 " pdb=" PA ADP C 402 " pdb=" O2A ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 25.57 -85.57 1 2.00e+01 2.50e-03 2.21e+01 ... (remaining 8936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1168 0.030 - 0.061: 697 0.061 - 0.091: 254 0.091 - 0.121: 111 0.121 - 0.152: 12 Chirality restraints: 2242 Sorted by residual: chirality pdb=" C2' ADP A 402 " pdb=" C1' ADP A 402 " pdb=" C3' ADP A 402 " pdb=" O2' ADP A 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" C2' ADP B 402 " pdb=" C1' ADP B 402 " pdb=" C3' ADP B 402 " pdb=" O2' ADP B 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE B 165 " pdb=" N ILE B 165 " pdb=" C ILE B 165 " pdb=" CB ILE B 165 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 2239 not shown) Planarity restraints: 2574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 90 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C PHE C 90 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE C 90 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR C 91 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 332 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO B 333 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 333 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 333 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 257 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO C 258 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 258 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 258 " 0.023 5.00e-02 4.00e+02 ... (remaining 2571 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 160 2.56 - 3.14: 12024 3.14 - 3.73: 22032 3.73 - 4.31: 31464 4.31 - 4.90: 53365 Nonbonded interactions: 119045 Sorted by model distance: nonbonded pdb="MG MG E 401 " pdb=" O3B ADP E 402 " model vdw 1.970 2.170 nonbonded pdb=" OE1 GLN B 137 " pdb="MG MG B 401 " model vdw 2.052 2.170 nonbonded pdb=" OE1 GLN C 137 " pdb="MG MG C 401 " model vdw 2.131 2.170 nonbonded pdb="MG MG A 401 " pdb=" O1B ADP A 402 " model vdw 2.131 2.170 nonbonded pdb=" N ASP A 179 " pdb=" OD1 ASP A 179 " model vdw 2.137 3.120 ... (remaining 119040 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 153 or (resid 154 and (name N or na \ me CA or name C or name O or name CB )) or resid 155 through 212 or (resid 213 t \ hrough 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 302 or (resid 303 through 304 and (name N or name CA or name C or name \ O or name CB )) or resid 305 through 402)) selection = (chain 'B' and (resid 5 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 153 or (resid 154 and (name N or na \ me CA or name C or name O or name CB )) or resid 155 through 212 or (resid 213 t \ hrough 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 302 or (resid 303 through 304 and (name N or name CA or name C or name \ O or name CB )) or resid 305 through 402)) selection = (chain 'C' and (resid 5 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 124 or (resid 125 and (name N or na \ me CA or name C or name O or name CB )) or resid 126 through 213 or (resid 214 a \ nd (name N or name CA or name C or name O or name CB )) or resid 215 through 302 \ or (resid 303 through 304 and (name N or name CA or name C or name O or name CB \ )) or resid 305 through 402)) selection = (chain 'D' and (resid 5 through 124 or (resid 125 and (name N or name CA or name \ C or name O or name CB )) or resid 126 through 213 or (resid 214 and (name N or \ name CA or name C or name O or name CB )) or resid 215 through 303 or (resid 30 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 305 through \ 402)) selection = (chain 'E' and (resid 5 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 124 or (resid 125 and (name N or na \ me CA or name C or name O or name CB )) or resid 126 through 153 or (resid 154 a \ nd (name N or name CA or name C or name O or name CB )) or resid 155 through 212 \ or (resid 213 through 214 and (name N or name CA or name C or name O or name CB \ )) or resid 215 through 302 or (resid 303 through 304 and (name N or name CA or \ name C or name O or name CB )) or resid 305 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.950 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14845 Z= 0.198 Angle : 0.662 8.810 20146 Z= 0.360 Chirality : 0.045 0.152 2242 Planarity : 0.004 0.040 2574 Dihedral : 13.362 91.540 5519 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 8.39 % Allowed : 9.23 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.13 (0.16), residues: 1840 helix: -2.02 (0.17), residues: 660 sheet: -3.02 (0.28), residues: 265 loop : -3.23 (0.17), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 62 TYR 0.010 0.001 TYR E 294 PHE 0.012 0.001 PHE B 255 TRP 0.011 0.001 TRP B 340 HIS 0.003 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00436 (14845) covalent geometry : angle 0.66172 (20146) hydrogen bonds : bond 0.16510 ( 517) hydrogen bonds : angle 6.87554 ( 1395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 177 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7615 (p0) REVERT: A 82 MET cc_start: 0.8438 (tpp) cc_final: 0.8030 (tpt) REVERT: A 101 HIS cc_start: 0.8890 (m-70) cc_final: 0.8582 (m90) REVERT: A 180 LEU cc_start: 0.8921 (tp) cc_final: 0.8568 (tp) REVERT: A 192 ILE cc_start: 0.9431 (tp) cc_final: 0.8877 (tt) REVERT: A 303 THR cc_start: 0.9432 (OUTLIER) cc_final: 0.9094 (p) REVERT: A 337 TYR cc_start: 0.8019 (m-80) cc_final: 0.7712 (m-80) REVERT: B 12 ASN cc_start: 0.8881 (t0) cc_final: 0.8016 (p0) REVERT: B 68 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8711 (ttmm) REVERT: B 142 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8923 (mp) REVERT: B 167 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: B 195 GLU cc_start: 0.7856 (pt0) cc_final: 0.7543 (pt0) REVERT: C 12 ASN cc_start: 0.8564 (t0) cc_final: 0.8296 (p0) REVERT: C 16 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9082 (mt) REVERT: C 116 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7617 (mtt90) REVERT: C 176 MET cc_start: 0.8588 (mmm) cc_final: 0.7877 (mmt) REVERT: C 180 LEU cc_start: 0.9151 (tp) cc_final: 0.8887 (tp) REVERT: D 16 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9179 (mt) REVERT: D 43 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8951 (m) REVERT: D 47 MET cc_start: 0.7250 (mmm) cc_final: 0.6933 (mmt) REVERT: D 49 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: D 116 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7762 (mtp85) REVERT: D 218 TYR cc_start: 0.9261 (OUTLIER) cc_final: 0.8855 (p90) REVERT: D 227 MET cc_start: 0.8147 (mmm) cc_final: 0.7894 (tpt) REVERT: E 43 VAL cc_start: 0.8171 (OUTLIER) cc_final: 0.7861 (p) REVERT: E 44 MET cc_start: 0.8205 (mmt) cc_final: 0.6818 (mpp) REVERT: E 142 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9105 (mp) REVERT: E 283 MET cc_start: 0.8555 (mmt) cc_final: 0.8123 (mmt) REVERT: E 286 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7475 (t0) outliers start: 130 outliers final: 64 residues processed: 293 average time/residue: 0.1011 time to fit residues: 46.4266 Evaluate side-chains 197 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 118 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 78 ASN A 161 HIS A 162 ASN A 173 HIS A 252 ASN A 275 HIS A 353 GLN B 78 ASN B 121 GLN B 162 ASN B 173 HIS B 296 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 246 GLN D 41 GLN D 111 ASN D 246 GLN D 353 GLN E 49 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 162 ASN E 275 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.070528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.060613 restraints weight = 34649.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.062239 restraints weight = 19930.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.063345 restraints weight = 13138.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.064109 restraints weight = 9693.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.064592 restraints weight = 7752.034| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14845 Z= 0.250 Angle : 0.700 9.467 20146 Z= 0.347 Chirality : 0.048 0.155 2242 Planarity : 0.005 0.035 2574 Dihedral : 10.378 91.895 2210 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 6.65 % Allowed : 12.52 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.18), residues: 1840 helix: -1.32 (0.19), residues: 680 sheet: -2.65 (0.30), residues: 275 loop : -2.35 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 177 TYR 0.010 0.001 TYR B 198 PHE 0.015 0.002 PHE B 255 TRP 0.011 0.002 TRP B 340 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00582 (14845) covalent geometry : angle 0.69985 (20146) hydrogen bonds : bond 0.04058 ( 517) hydrogen bonds : angle 5.61020 ( 1395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 124 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: A 80 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7365 (p0) REVERT: A 82 MET cc_start: 0.8493 (tpp) cc_final: 0.8061 (tpt) REVERT: A 101 HIS cc_start: 0.8937 (m-70) cc_final: 0.8633 (m90) REVERT: A 180 LEU cc_start: 0.8947 (tp) cc_final: 0.8634 (tp) REVERT: B 142 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8840 (mp) REVERT: B 167 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: B 313 MET cc_start: 0.8524 (tpp) cc_final: 0.7956 (mtp) REVERT: C 12 ASN cc_start: 0.8723 (t0) cc_final: 0.8128 (p0) REVERT: C 16 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9184 (mt) REVERT: C 72 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: C 116 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7566 (mtt90) REVERT: C 162 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8824 (m-40) REVERT: C 176 MET cc_start: 0.8531 (mmm) cc_final: 0.7826 (mmt) REVERT: C 180 LEU cc_start: 0.9242 (tp) cc_final: 0.8997 (tp) REVERT: C 288 ASP cc_start: 0.7858 (p0) cc_final: 0.7466 (t0) REVERT: D 47 MET cc_start: 0.7151 (mmm) cc_final: 0.6671 (mmt) REVERT: D 49 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: D 116 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7849 (mtp85) REVERT: D 227 MET cc_start: 0.8057 (mmm) cc_final: 0.7749 (tpt) REVERT: E 43 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7852 (p) REVERT: E 44 MET cc_start: 0.8068 (mmt) cc_final: 0.6837 (mpp) REVERT: E 142 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9056 (mp) REVERT: E 152 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8949 (t) REVERT: E 162 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.7898 (m110) outliers start: 103 outliers final: 64 residues processed: 213 average time/residue: 0.0890 time to fit residues: 30.9279 Evaluate side-chains 191 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 113 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 111 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 0.0980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN C 275 HIS D 275 HIS E 78 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.073775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.064015 restraints weight = 34139.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.065686 restraints weight = 19164.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.066829 restraints weight = 12513.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.067604 restraints weight = 9092.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.068128 restraints weight = 7185.931| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14845 Z= 0.106 Angle : 0.599 8.660 20146 Z= 0.292 Chirality : 0.044 0.152 2242 Planarity : 0.004 0.036 2574 Dihedral : 9.432 84.311 2161 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.97 % Allowed : 13.75 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.19), residues: 1840 helix: -0.78 (0.20), residues: 680 sheet: -2.36 (0.30), residues: 285 loop : -1.84 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.008 0.001 TYR D 306 PHE 0.013 0.001 PHE B 352 TRP 0.010 0.001 TRP A 340 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00241 (14845) covalent geometry : angle 0.59887 (20146) hydrogen bonds : bond 0.03076 ( 517) hydrogen bonds : angle 5.08863 ( 1395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 136 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7324 (mmm) cc_final: 0.7102 (mmm) REVERT: A 57 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7956 (tp30) REVERT: A 80 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7173 (p0) REVERT: A 82 MET cc_start: 0.8327 (tpp) cc_final: 0.7964 (tpt) REVERT: A 101 HIS cc_start: 0.8768 (m-70) cc_final: 0.8556 (m90) REVERT: A 180 LEU cc_start: 0.8931 (tp) cc_final: 0.8582 (tp) REVERT: B 124 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8718 (m-80) REVERT: B 313 MET cc_start: 0.8352 (tpp) cc_final: 0.8009 (ttm) REVERT: C 12 ASN cc_start: 0.8627 (t0) cc_final: 0.7702 (p0) REVERT: C 16 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9151 (mt) REVERT: C 116 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7471 (mtt90) REVERT: C 134 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8856 (m) REVERT: C 176 MET cc_start: 0.8470 (mmm) cc_final: 0.7848 (mmt) REVERT: D 47 MET cc_start: 0.7029 (mmm) cc_final: 0.6566 (mmt) REVERT: D 49 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: D 99 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: D 116 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7693 (mtp85) REVERT: D 191 LYS cc_start: 0.9056 (tmtt) cc_final: 0.8559 (ttmt) REVERT: D 227 MET cc_start: 0.8049 (mmm) cc_final: 0.7766 (tpt) REVERT: E 43 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7741 (p) REVERT: E 44 MET cc_start: 0.8039 (mmt) cc_final: 0.6820 (mpp) REVERT: E 132 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7776 (ppp) REVERT: E 142 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8882 (mp) REVERT: E 217 CYS cc_start: 0.9041 (m) cc_final: 0.8318 (m) REVERT: E 289 ILE cc_start: 0.9245 (mt) cc_final: 0.8975 (tt) outliers start: 77 outliers final: 38 residues processed: 195 average time/residue: 0.0914 time to fit residues: 28.8442 Evaluate side-chains 169 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 137 optimal weight: 0.1980 chunk 65 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 183 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 111 ASN ** 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 = 0.2948 r_free = 0.2948 target = 0.073604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.063877 restraints weight = 34123.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.065559 restraints weight = 19162.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.066699 restraints weight = 12412.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.067470 restraints weight = 9010.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.067983 restraints weight = 7093.849| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14845 Z= 0.128 Angle : 0.605 7.387 20146 Z= 0.293 Chirality : 0.045 0.157 2242 Planarity : 0.004 0.036 2574 Dihedral : 8.537 79.317 2125 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.71 % Allowed : 14.53 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.20), residues: 1840 helix: -0.53 (0.21), residues: 680 sheet: -2.15 (0.31), residues: 285 loop : -1.52 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.013 0.001 TYR B 166 PHE 0.015 0.001 PHE B 352 TRP 0.009 0.001 TRP A 340 HIS 0.005 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00296 (14845) covalent geometry : angle 0.60508 (20146) hydrogen bonds : bond 0.02974 ( 517) hydrogen bonds : angle 4.93584 ( 1395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 126 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8940 (mt) REVERT: A 47 MET cc_start: 0.7340 (mmm) cc_final: 0.7046 (mmm) REVERT: A 57 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7950 (tp30) REVERT: A 80 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7294 (p0) REVERT: A 82 MET cc_start: 0.8323 (tpp) cc_final: 0.8021 (tpt) REVERT: A 180 LEU cc_start: 0.8866 (tp) cc_final: 0.8637 (tp) REVERT: B 124 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8706 (m-80) REVERT: B 283 MET cc_start: 0.8590 (mmm) cc_final: 0.8152 (mmt) REVERT: C 72 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7123 (tt0) REVERT: C 116 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7268 (mtt90) REVERT: C 134 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8886 (m) REVERT: C 176 MET cc_start: 0.8537 (mmm) cc_final: 0.7855 (mmt) REVERT: C 180 LEU cc_start: 0.9160 (tp) cc_final: 0.8921 (tp) REVERT: C 288 ASP cc_start: 0.7690 (p0) cc_final: 0.7417 (t0) REVERT: D 47 MET cc_start: 0.7059 (mmm) cc_final: 0.6578 (mmt) REVERT: D 49 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: D 99 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: D 116 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7709 (mtp85) REVERT: D 191 LYS cc_start: 0.9069 (tmtt) cc_final: 0.8561 (ttmt) REVERT: D 227 MET cc_start: 0.7834 (mmm) cc_final: 0.7578 (tpt) REVERT: E 43 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7719 (p) REVERT: E 44 MET cc_start: 0.8075 (mmt) cc_final: 0.6797 (mpp) REVERT: E 132 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7848 (ppp) REVERT: E 142 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8890 (mp) REVERT: E 217 CYS cc_start: 0.9079 (m) cc_final: 0.8334 (m) outliers start: 73 outliers final: 42 residues processed: 187 average time/residue: 0.0936 time to fit residues: 28.2074 Evaluate side-chains 173 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 118 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 164 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 chunk 151 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 175 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN ** E 111 ASN ** 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 = 0.2963 r_free = 0.2963 target = 0.074354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.064651 restraints weight = 33861.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.066365 restraints weight = 18951.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.067502 restraints weight = 12270.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.068255 restraints weight = 8896.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.068803 restraints weight = 7033.076| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14845 Z= 0.114 Angle : 0.586 9.398 20146 Z= 0.282 Chirality : 0.044 0.146 2242 Planarity : 0.003 0.035 2574 Dihedral : 8.063 73.284 2117 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.39 % Allowed : 15.62 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.20), residues: 1840 helix: -0.36 (0.21), residues: 680 sheet: -1.98 (0.31), residues: 285 loop : -1.34 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 62 TYR 0.010 0.001 TYR B 166 PHE 0.013 0.001 PHE B 352 TRP 0.008 0.001 TRP A 340 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00265 (14845) covalent geometry : angle 0.58633 (20146) hydrogen bonds : bond 0.02781 ( 517) hydrogen bonds : angle 4.81966 ( 1395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 124 time to evaluate : 0.562 Fit side-chains REVERT: A 16 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8876 (mt) REVERT: A 47 MET cc_start: 0.7441 (mmm) cc_final: 0.7136 (mmm) REVERT: A 57 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7948 (tp30) REVERT: A 80 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7253 (p0) REVERT: A 82 MET cc_start: 0.8317 (tpp) cc_final: 0.8062 (tpt) REVERT: B 124 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8714 (m-80) REVERT: C 116 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7220 (mtt90) REVERT: C 134 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8881 (m) REVERT: C 176 MET cc_start: 0.8525 (mmm) cc_final: 0.7814 (mmt) REVERT: C 288 ASP cc_start: 0.7717 (p0) cc_final: 0.7404 (t0) REVERT: D 47 MET cc_start: 0.7011 (mmm) cc_final: 0.6520 (mmt) REVERT: D 49 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: D 99 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: D 116 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7709 (mtp85) REVERT: D 191 LYS cc_start: 0.9063 (tmtt) cc_final: 0.8552 (ttmt) REVERT: D 227 MET cc_start: 0.7820 (mmm) cc_final: 0.7543 (tpt) REVERT: D 289 ILE cc_start: 0.9169 (mt) cc_final: 0.8912 (tt) REVERT: E 43 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7690 (p) REVERT: E 44 MET cc_start: 0.8056 (mmt) cc_final: 0.6689 (mpp) REVERT: E 142 LEU cc_start: 0.9282 (tp) cc_final: 0.8825 (mp) REVERT: E 289 ILE cc_start: 0.9221 (mt) cc_final: 0.8937 (tt) outliers start: 68 outliers final: 41 residues processed: 179 average time/residue: 0.0892 time to fit residues: 25.9495 Evaluate side-chains 170 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 119 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 122 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 182 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS E 78 ASN ** E 111 ASN ** 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 = 0.2940 r_free = 0.2940 target = 0.073124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.063324 restraints weight = 34222.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.064969 restraints weight = 19436.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.066099 restraints weight = 12853.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.066895 restraints weight = 9334.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.067439 restraints weight = 7355.195| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14845 Z= 0.163 Angle : 0.615 10.415 20146 Z= 0.296 Chirality : 0.045 0.169 2242 Planarity : 0.004 0.034 2574 Dihedral : 7.676 70.566 2108 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.39 % Allowed : 16.27 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.20), residues: 1840 helix: -0.34 (0.21), residues: 680 sheet: -1.94 (0.32), residues: 285 loop : -1.26 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.010 0.001 TYR B 166 PHE 0.015 0.001 PHE B 352 TRP 0.008 0.001 TRP A 340 HIS 0.006 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00381 (14845) covalent geometry : angle 0.61484 (20146) hydrogen bonds : bond 0.02973 ( 517) hydrogen bonds : angle 4.83286 ( 1395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 114 time to evaluate : 0.577 Fit side-chains REVERT: A 16 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8864 (mt) REVERT: A 47 MET cc_start: 0.7462 (mmm) cc_final: 0.7147 (mmm) REVERT: A 57 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7967 (tp30) REVERT: A 80 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7364 (p0) REVERT: A 82 MET cc_start: 0.8374 (tpp) cc_final: 0.8106 (tpt) REVERT: A 123 MET cc_start: 0.8951 (tpp) cc_final: 0.8548 (mmt) REVERT: A 124 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8162 (m-10) REVERT: A 180 LEU cc_start: 0.8743 (tp) cc_final: 0.8433 (tp) REVERT: B 124 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8708 (m-80) REVERT: C 72 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7122 (tt0) REVERT: C 116 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7779 (mtp85) REVERT: C 134 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8901 (m) REVERT: C 176 MET cc_start: 0.8518 (mmm) cc_final: 0.7830 (mmt) REVERT: C 288 ASP cc_start: 0.7750 (p0) cc_final: 0.7462 (t0) REVERT: D 47 MET cc_start: 0.7034 (mmm) cc_final: 0.6531 (mmt) REVERT: D 49 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: D 99 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7270 (mt-10) REVERT: D 116 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7774 (mtp85) REVERT: D 191 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8593 (ttmt) REVERT: D 227 MET cc_start: 0.7839 (mmm) cc_final: 0.7562 (tpt) REVERT: E 43 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7701 (p) REVERT: E 44 MET cc_start: 0.8067 (mmt) cc_final: 0.6696 (mpp) REVERT: E 132 MET cc_start: 0.8250 (ppp) cc_final: 0.8026 (ppp) REVERT: E 142 LEU cc_start: 0.9330 (tp) cc_final: 0.8865 (mp) outliers start: 68 outliers final: 47 residues processed: 170 average time/residue: 0.0945 time to fit residues: 26.0449 Evaluate side-chains 172 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 113 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 163 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS C 49 GLN E 78 ASN ** E 111 ASN ** 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 = 0.2978 r_free = 0.2978 target = 0.075205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.065506 restraints weight = 33478.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.067204 restraints weight = 18846.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.068356 restraints weight = 12267.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.069106 restraints weight = 8916.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.069660 restraints weight = 7086.251| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14845 Z= 0.096 Angle : 0.574 10.657 20146 Z= 0.273 Chirality : 0.043 0.145 2242 Planarity : 0.003 0.034 2574 Dihedral : 7.248 63.673 2107 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.55 % Allowed : 17.17 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.20), residues: 1840 helix: -0.17 (0.21), residues: 680 sheet: -1.87 (0.32), residues: 285 loop : -1.09 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 256 TYR 0.008 0.001 TYR D 143 PHE 0.014 0.001 PHE B 352 TRP 0.009 0.001 TRP B 356 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00221 (14845) covalent geometry : angle 0.57357 (20146) hydrogen bonds : bond 0.02567 ( 517) hydrogen bonds : angle 4.67499 ( 1395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 127 time to evaluate : 0.480 Fit side-chains REVERT: A 47 MET cc_start: 0.7425 (mmm) cc_final: 0.7142 (mmm) REVERT: A 57 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7959 (tp30) REVERT: A 124 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.8113 (m-10) REVERT: B 224 GLU cc_start: 0.7618 (tp30) cc_final: 0.7368 (tp30) REVERT: C 72 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: C 116 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7548 (mtt90) REVERT: C 134 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8793 (m) REVERT: C 176 MET cc_start: 0.8487 (mmm) cc_final: 0.7788 (mmt) REVERT: D 47 MET cc_start: 0.6928 (mmm) cc_final: 0.6453 (mmt) REVERT: D 49 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: D 99 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: D 191 LYS cc_start: 0.8999 (tmtt) cc_final: 0.8499 (ttmt) REVERT: D 227 MET cc_start: 0.7838 (mmm) cc_final: 0.7594 (tpt) REVERT: D 289 ILE cc_start: 0.9099 (mt) cc_final: 0.8851 (tt) REVERT: E 43 VAL cc_start: 0.8092 (OUTLIER) cc_final: 0.7655 (p) REVERT: E 44 MET cc_start: 0.8049 (mmt) cc_final: 0.6693 (mpp) REVERT: E 132 MET cc_start: 0.8152 (ppp) cc_final: 0.7916 (ppp) REVERT: E 142 LEU cc_start: 0.9276 (tp) cc_final: 0.8849 (mp) REVERT: E 217 CYS cc_start: 0.9056 (m) cc_final: 0.8369 (m) outliers start: 55 outliers final: 38 residues processed: 173 average time/residue: 0.0869 time to fit residues: 24.7652 Evaluate side-chains 163 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 177 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 111 ASN ** 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 = 0.2964 r_free = 0.2964 target = 0.074454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.064692 restraints weight = 33665.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.066372 restraints weight = 19040.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.067477 restraints weight = 12443.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.068270 restraints weight = 9117.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.068800 restraints weight = 7212.545| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14845 Z= 0.125 Angle : 0.594 11.446 20146 Z= 0.283 Chirality : 0.044 0.148 2242 Planarity : 0.003 0.031 2574 Dihedral : 6.950 62.288 2099 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.81 % Allowed : 17.37 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.20), residues: 1840 helix: -0.12 (0.21), residues: 680 sheet: -1.86 (0.32), residues: 285 loop : -1.03 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 256 TYR 0.006 0.001 TYR D 306 PHE 0.025 0.001 PHE B 352 TRP 0.007 0.001 TRP A 340 HIS 0.005 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00291 (14845) covalent geometry : angle 0.59375 (20146) hydrogen bonds : bond 0.02715 ( 517) hydrogen bonds : angle 4.66430 ( 1395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 119 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7449 (mmm) cc_final: 0.7128 (mmm) REVERT: A 57 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: A 124 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.8155 (m-10) REVERT: B 224 GLU cc_start: 0.7653 (tp30) cc_final: 0.7413 (tp30) REVERT: C 72 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6992 (tt0) REVERT: C 116 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7590 (mtt90) REVERT: C 134 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8812 (m) REVERT: C 176 MET cc_start: 0.8490 (mmm) cc_final: 0.7829 (mmt) REVERT: D 47 MET cc_start: 0.6923 (mmm) cc_final: 0.6457 (mmt) REVERT: D 49 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: D 99 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: D 191 LYS cc_start: 0.8963 (tmtt) cc_final: 0.8514 (ttmt) REVERT: D 227 MET cc_start: 0.7843 (mmm) cc_final: 0.7578 (tpt) REVERT: D 289 ILE cc_start: 0.9139 (mt) cc_final: 0.8888 (tt) REVERT: E 43 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7662 (p) REVERT: E 44 MET cc_start: 0.8048 (mmt) cc_final: 0.6668 (mpp) REVERT: E 132 MET cc_start: 0.8220 (ppp) cc_final: 0.7973 (ppp) REVERT: E 142 LEU cc_start: 0.9339 (tp) cc_final: 0.8865 (mp) REVERT: E 289 ILE cc_start: 0.9248 (mt) cc_final: 0.9024 (tt) outliers start: 59 outliers final: 41 residues processed: 166 average time/residue: 0.0942 time to fit residues: 25.5056 Evaluate side-chains 164 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 115 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.075765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.065997 restraints weight = 33670.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.067722 restraints weight = 18923.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.068881 restraints weight = 12297.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.069638 restraints weight = 8933.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.070184 restraints weight = 7108.744| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14845 Z= 0.098 Angle : 0.578 11.948 20146 Z= 0.274 Chirality : 0.044 0.146 2242 Planarity : 0.003 0.030 2574 Dihedral : 6.550 59.088 2097 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.23 % Allowed : 18.08 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.20), residues: 1840 helix: -0.01 (0.21), residues: 680 sheet: -1.86 (0.31), residues: 285 loop : -0.91 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.006 0.001 TYR D 143 PHE 0.021 0.001 PHE B 352 TRP 0.009 0.001 TRP B 356 HIS 0.004 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00224 (14845) covalent geometry : angle 0.57845 (20146) hydrogen bonds : bond 0.02564 ( 517) hydrogen bonds : angle 4.57081 ( 1395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 121 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7437 (mmm) cc_final: 0.7126 (mmm) REVERT: A 57 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7950 (tp30) REVERT: A 124 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: B 123 MET cc_start: 0.8087 (mmm) cc_final: 0.7829 (tpp) REVERT: B 313 MET cc_start: 0.8046 (mtp) cc_final: 0.7823 (mtp) REVERT: C 72 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7012 (tt0) REVERT: C 134 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8922 (m) REVERT: C 176 MET cc_start: 0.8462 (mmm) cc_final: 0.7792 (mmt) REVERT: D 47 MET cc_start: 0.6842 (mmm) cc_final: 0.6405 (mmt) REVERT: D 49 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: D 99 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: D 191 LYS cc_start: 0.8930 (tmtt) cc_final: 0.8465 (ttmt) REVERT: D 227 MET cc_start: 0.7913 (mmm) cc_final: 0.7689 (tpt) REVERT: D 289 ILE cc_start: 0.9096 (mt) cc_final: 0.8813 (tt) REVERT: E 43 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7635 (p) REVERT: E 44 MET cc_start: 0.8029 (mmt) cc_final: 0.6622 (mpp) REVERT: E 132 MET cc_start: 0.8246 (ppp) cc_final: 0.7986 (ppp) REVERT: E 142 LEU cc_start: 0.9323 (tp) cc_final: 0.8871 (mp) REVERT: E 289 ILE cc_start: 0.9206 (mt) cc_final: 0.8989 (tt) outliers start: 50 outliers final: 39 residues processed: 164 average time/residue: 0.0905 time to fit residues: 24.5347 Evaluate side-chains 160 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 87 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 121 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 151 optimal weight: 0.0970 chunk 164 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.076675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.067012 restraints weight = 33369.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.068712 restraints weight = 18674.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.069835 restraints weight = 12106.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.070630 restraints weight = 8840.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.071162 restraints weight = 6962.759| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14845 Z= 0.092 Angle : 0.581 12.669 20146 Z= 0.275 Chirality : 0.043 0.177 2242 Planarity : 0.003 0.030 2574 Dihedral : 6.174 58.821 2091 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.97 % Allowed : 18.59 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.20), residues: 1840 helix: 0.08 (0.21), residues: 680 sheet: -1.83 (0.31), residues: 285 loop : -0.78 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.006 0.001 TYR D 143 PHE 0.020 0.001 PHE B 352 TRP 0.010 0.001 TRP B 356 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00208 (14845) covalent geometry : angle 0.58053 (20146) hydrogen bonds : bond 0.02504 ( 517) hydrogen bonds : angle 4.50747 ( 1395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 0.531 Fit side-chains REVERT: A 47 MET cc_start: 0.7429 (mmm) cc_final: 0.7108 (mmm) REVERT: A 57 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: A 124 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8109 (m-10) REVERT: B 123 MET cc_start: 0.8039 (mmm) cc_final: 0.7833 (tpp) REVERT: C 72 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: C 134 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8857 (m) REVERT: C 176 MET cc_start: 0.8396 (mmm) cc_final: 0.7730 (mmt) REVERT: D 99 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: D 191 LYS cc_start: 0.8880 (tmtt) cc_final: 0.8423 (ttmt) REVERT: D 227 MET cc_start: 0.7909 (mmm) cc_final: 0.7695 (tpt) REVERT: D 289 ILE cc_start: 0.9052 (mt) cc_final: 0.8764 (tt) REVERT: E 43 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7761 (p) REVERT: E 44 MET cc_start: 0.8093 (mmt) cc_final: 0.6604 (mpp) REVERT: E 132 MET cc_start: 0.8263 (ppp) cc_final: 0.8014 (ppp) REVERT: E 142 LEU cc_start: 0.9318 (tp) cc_final: 0.8874 (mp) REVERT: E 289 ILE cc_start: 0.9197 (mt) cc_final: 0.8952 (tt) REVERT: E 355 MET cc_start: 0.8008 (mmm) cc_final: 0.7749 (mmm) outliers start: 46 outliers final: 31 residues processed: 166 average time/residue: 0.0894 time to fit residues: 24.2809 Evaluate side-chains 155 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 39 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 64 optimal weight: 0.0570 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN C 353 GLN E 78 ASN ** E 111 ASN ** 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 = 0.2929 r_free = 0.2929 target = 0.072624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.062700 restraints weight = 34263.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.064351 restraints weight = 19660.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.065473 restraints weight = 12963.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.066242 restraints weight = 9502.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.066769 restraints weight = 7583.309| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14845 Z= 0.219 Angle : 0.685 13.287 20146 Z= 0.326 Chirality : 0.048 0.220 2242 Planarity : 0.004 0.029 2574 Dihedral : 6.413 59.496 2084 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.78 % Allowed : 19.11 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.20), residues: 1840 helix: -0.06 (0.21), residues: 670 sheet: -1.76 (0.33), residues: 275 loop : -0.86 (0.22), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 290 TYR 0.010 0.001 TYR B 198 PHE 0.021 0.002 PHE B 352 TRP 0.010 0.001 TRP A 86 HIS 0.005 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00513 (14845) covalent geometry : angle 0.68507 (20146) hydrogen bonds : bond 0.03205 ( 517) hydrogen bonds : angle 4.79067 ( 1395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1810.66 seconds wall clock time: 32 minutes 19.15 seconds (1939.15 seconds total)