Starting phenix.real_space_refine on Tue Dec 31 02:28:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bt7_30171/12_2024/7bt7_30171.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bt7_30171/12_2024/7bt7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7bt7_30171/12_2024/7bt7_30171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bt7_30171/12_2024/7bt7_30171.map" model { file = "/net/cci-nas-00/data/ceres_data/7bt7_30171/12_2024/7bt7_30171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bt7_30171/12_2024/7bt7_30171.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 9.01, per 1000 atoms: 0.62 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: 3.95 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.96 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: 4.50 Time building geometry restraints manager: 4.31 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 374 or resid 401 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 374 or resid 401 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 374 or resid 401 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 \ 374 or resid 401 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 374 or resid 401 through 40 \ 2)) } 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: 1.760 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.300 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.370 ------------------------------------------------------------------------------- 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= 0.286 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 : 12.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.001 TRP B 340 HIS 0.003 0.001 HIS C 87 PHE 0.012 0.001 PHE B 255 TYR 0.010 0.001 TYR E 294 ARG 0.004 0.000 ARG C 62 *********************** 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 : 1.586 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: 0.8567 (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: 0.7876 (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: 0.8077 (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: 0.8554 (mmt) cc_final: 0.8122 (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: 0.2284 time to fit residues: 103.4812 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 : 1.829 ------------------------------------------------------------------------------- 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 156 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 56 optimal weight: 0.0040 chunk 88 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN A 173 HIS A 252 ASN A 275 HIS A 353 GLN B 121 GLN B 162 ASN B 173 HIS B 296 ASN C 111 ASN C 246 GLN C 275 HIS D 41 GLN D 246 GLN D 353 GLN E 49 GLN E 115 ASN E 162 ASN E 275 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14845 Z= 0.224 Angle : 0.637 7.758 20146 Z= 0.315 Chirality : 0.046 0.150 2242 Planarity : 0.004 0.033 2574 Dihedral : 10.051 87.681 2210 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 6.07 % Allowed : 11.75 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.19), residues: 1840 helix: -1.17 (0.19), residues: 680 sheet: -2.69 (0.29), residues: 285 loop : -2.26 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.004 0.001 HIS C 87 PHE 0.010 0.001 PHE B 255 TYR 0.011 0.001 TYR C 166 ARG 0.003 0.000 ARG B 177 *********************** 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: 94 poor density : 133 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8031 (tp30) REVERT: A 80 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7309 (p0) REVERT: A 82 MET cc_start: 0.8498 (tpp) cc_final: 0.8126 (tpt) REVERT: A 101 HIS cc_start: 0.8871 (m-70) cc_final: 0.8615 (m90) REVERT: A 143 TYR cc_start: 0.8562 (m-10) cc_final: 0.8361 (m-10) REVERT: A 180 LEU cc_start: 0.8906 (tp) cc_final: 0.8624 (tp) REVERT: A 337 TYR cc_start: 0.8038 (m-80) cc_final: 0.7817 (m-80) REVERT: B 167 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: B 195 GLU cc_start: 0.7792 (pt0) cc_final: 0.7440 (pt0) REVERT: B 313 MET cc_start: 0.8469 (tpp) cc_final: 0.7941 (mtp) REVERT: C 12 ASN cc_start: 0.8661 (t0) cc_final: 0.8028 (p0) REVERT: C 16 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9152 (mt) REVERT: C 72 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: C 116 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7488 (mtt90) REVERT: C 134 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8876 (m) REVERT: C 180 LEU cc_start: 0.9181 (tp) cc_final: 0.8908 (tp) REVERT: C 288 ASP cc_start: 0.7881 (p0) cc_final: 0.7447 (t0) REVERT: D 47 MET cc_start: 0.7222 (mmm) cc_final: 0.6693 (mmt) REVERT: D 49 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: D 116 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7724 (mtp85) REVERT: D 191 LYS cc_start: 0.9206 (tmtt) cc_final: 0.8629 (ttmt) REVERT: D 218 TYR cc_start: 0.9251 (OUTLIER) cc_final: 0.8756 (p90) REVERT: D 227 MET cc_start: 0.8093 (mmm) cc_final: 0.7817 (tpt) REVERT: E 43 VAL cc_start: 0.8134 (OUTLIER) cc_final: 0.7779 (p) REVERT: E 44 MET cc_start: 0.8239 (mmt) cc_final: 0.6861 (mpp) REVERT: E 142 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8945 (mp) REVERT: E 152 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8939 (t) REVERT: E 162 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.7886 (m110) outliers start: 94 outliers final: 51 residues processed: 213 average time/residue: 0.2221 time to fit residues: 75.3692 Evaluate side-chains 181 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 116 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 89 THR 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 260 THR Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 338 SER 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 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 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 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 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 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 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 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 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 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 93 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS B 78 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14845 Z= 0.315 Angle : 0.656 8.836 20146 Z= 0.320 Chirality : 0.047 0.150 2242 Planarity : 0.004 0.035 2574 Dihedral : 9.387 86.511 2146 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 5.81 % Allowed : 13.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.19), residues: 1840 helix: -0.88 (0.20), residues: 680 sheet: -2.32 (0.31), residues: 275 loop : -1.82 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 340 HIS 0.004 0.001 HIS C 87 PHE 0.015 0.001 PHE B 352 TYR 0.010 0.001 TYR E 143 ARG 0.003 0.000 ARG B 62 *********************** 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 207 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 117 time to evaluate : 1.700 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7948 (tp30) REVERT: A 80 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7373 (p0) REVERT: A 82 MET cc_start: 0.8555 (tpp) cc_final: 0.8140 (tpt) REVERT: A 101 HIS cc_start: 0.8936 (m-70) cc_final: 0.8650 (m90) REVERT: A 180 LEU cc_start: 0.8991 (tp) cc_final: 0.8783 (tp) REVERT: A 337 TYR cc_start: 0.8066 (m-80) cc_final: 0.7684 (m-80) REVERT: B 167 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: B 313 MET cc_start: 0.8509 (tpp) cc_final: 0.8033 (mtp) REVERT: C 12 ASN cc_start: 0.8786 (t0) cc_final: 0.7854 (p0) REVERT: C 16 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9151 (mt) REVERT: C 72 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: C 116 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7467 (mtt90) REVERT: C 180 LEU cc_start: 0.9219 (tp) cc_final: 0.8912 (tp) REVERT: C 288 ASP cc_start: 0.7928 (p0) cc_final: 0.7512 (t0) REVERT: D 47 MET cc_start: 0.7244 (mmm) cc_final: 0.6682 (mmt) REVERT: D 49 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: D 99 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: D 116 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7766 (mtp85) REVERT: D 191 LYS cc_start: 0.9149 (tmtt) cc_final: 0.8650 (ttmt) REVERT: D 218 TYR cc_start: 0.9268 (OUTLIER) cc_final: 0.8905 (p90) REVERT: D 227 MET cc_start: 0.7863 (mmm) cc_final: 0.7569 (tpt) REVERT: E 43 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7742 (p) REVERT: E 44 MET cc_start: 0.8256 (mmt) cc_final: 0.6862 (mpp) REVERT: E 142 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8962 (mp) outliers start: 90 outliers final: 57 residues processed: 191 average time/residue: 0.2281 time to fit residues: 69.2369 Evaluate side-chains 182 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 113 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 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 190 MET 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 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 167 GLU 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 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 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 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 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 104 LEU 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 267 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 113 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 0.1980 chunk 160 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS E 78 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14845 Z= 0.168 Angle : 0.587 7.710 20146 Z= 0.285 Chirality : 0.044 0.145 2242 Planarity : 0.004 0.037 2574 Dihedral : 8.752 78.512 2137 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.58 % Allowed : 15.11 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1840 helix: -0.58 (0.20), residues: 680 sheet: -2.19 (0.31), residues: 285 loop : -1.52 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 340 HIS 0.004 0.001 HIS C 87 PHE 0.016 0.001 PHE E 223 TYR 0.007 0.001 TYR D 306 ARG 0.002 0.000 ARG A 290 *********************** 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 202 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 131 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8937 (mt) REVERT: A 57 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7981 (tp30) REVERT: A 80 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7363 (p0) REVERT: A 82 MET cc_start: 0.8352 (tpp) cc_final: 0.8005 (tpt) REVERT: A 180 LEU cc_start: 0.8849 (tp) cc_final: 0.8571 (tp) REVERT: A 337 TYR cc_start: 0.8023 (m-80) cc_final: 0.7700 (m-80) REVERT: B 259 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8464 (tm-30) REVERT: C 16 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9142 (mt) REVERT: C 116 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7284 (mtt90) REVERT: C 134 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8832 (m) REVERT: C 176 MET cc_start: 0.8591 (mmt) cc_final: 0.8207 (mmt) REVERT: C 180 LEU cc_start: 0.9159 (tp) cc_final: 0.8929 (tp) REVERT: C 288 ASP cc_start: 0.7888 (p0) cc_final: 0.7682 (p0) REVERT: D 47 MET cc_start: 0.7240 (mmm) cc_final: 0.6656 (mmt) REVERT: D 49 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: D 99 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: D 116 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7716 (mtp85) REVERT: D 191 LYS cc_start: 0.9076 (tmtt) cc_final: 0.8603 (ttmt) REVERT: D 227 MET cc_start: 0.7829 (mmm) cc_final: 0.7548 (tpt) REVERT: E 43 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7699 (p) REVERT: E 44 MET cc_start: 0.8206 (mmt) cc_final: 0.6779 (mpp) REVERT: E 142 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8852 (mp) outliers start: 71 outliers final: 41 residues processed: 185 average time/residue: 0.2207 time to fit residues: 64.5403 Evaluate side-chains 167 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 115 time to evaluate : 1.905 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 292 ASP 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 143 TYR 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 16 LEU 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 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 180 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 351 THR 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 71 ILE 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 267 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 133 optimal weight: 0.3980 chunk 73 optimal weight: 0.0070 chunk 152 optimal weight: 9.9990 chunk 123 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.6002 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14845 Z= 0.139 Angle : 0.574 8.804 20146 Z= 0.276 Chirality : 0.043 0.144 2242 Planarity : 0.003 0.037 2574 Dihedral : 7.957 70.073 2118 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.81 % Allowed : 16.27 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.20), residues: 1840 helix: -0.32 (0.21), residues: 680 sheet: -2.01 (0.31), residues: 285 loop : -1.28 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 356 HIS 0.005 0.000 HIS C 87 PHE 0.014 0.001 PHE B 352 TYR 0.011 0.001 TYR B 166 ARG 0.006 0.000 ARG A 290 *********************** 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 189 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 130 time to evaluate : 1.820 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8842 (mt) REVERT: A 57 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: A 80 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7318 (p0) REVERT: A 82 MET cc_start: 0.8319 (tpp) cc_final: 0.8010 (tpt) REVERT: A 337 TYR cc_start: 0.8019 (m-80) cc_final: 0.7689 (m-80) REVERT: B 10 CYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8620 (p) REVERT: C 116 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7194 (mtt90) REVERT: C 134 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8849 (m) REVERT: C 176 MET cc_start: 0.8566 (mmt) cc_final: 0.8211 (mmt) REVERT: C 180 LEU cc_start: 0.9042 (tp) cc_final: 0.8797 (tp) REVERT: C 288 ASP cc_start: 0.7914 (p0) cc_final: 0.7599 (t0) REVERT: D 47 MET cc_start: 0.7190 (mmm) cc_final: 0.6625 (mmt) REVERT: D 49 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: D 191 LYS cc_start: 0.9072 (tmtt) cc_final: 0.8608 (ttmt) REVERT: D 227 MET cc_start: 0.7874 (mmm) cc_final: 0.7640 (tpt) REVERT: E 43 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7643 (p) REVERT: E 44 MET cc_start: 0.8183 (mmt) cc_final: 0.6661 (mpp) REVERT: E 142 LEU cc_start: 0.9275 (tp) cc_final: 0.8856 (mp) REVERT: E 289 ILE cc_start: 0.9168 (mt) cc_final: 0.8921 (tt) outliers start: 59 outliers final: 40 residues processed: 177 average time/residue: 0.2205 time to fit residues: 62.5687 Evaluate side-chains 170 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 B residue 10 CYS 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 201 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 B residue 351 THR 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 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 260 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU 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 34 ILE 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 267 ILE 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 60 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 178 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2196 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= 0.185 Angle : 0.588 9.915 20146 Z= 0.281 Chirality : 0.044 0.146 2242 Planarity : 0.003 0.036 2574 Dihedral : 7.366 65.595 2104 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.39 % Allowed : 16.72 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.20), residues: 1840 helix: -0.25 (0.21), residues: 680 sheet: -1.93 (0.32), residues: 285 loop : -1.17 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 340 HIS 0.006 0.001 HIS A 87 PHE 0.015 0.001 PHE B 352 TYR 0.008 0.001 TYR B 166 ARG 0.003 0.000 ARG A 290 *********************** 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 190 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 122 time to evaluate : 1.736 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8827 (mt) REVERT: A 57 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7965 (tp30) REVERT: A 82 MET cc_start: 0.8373 (tpp) cc_final: 0.8089 (tpt) REVERT: A 124 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8233 (m-10) REVERT: A 337 TYR cc_start: 0.8003 (m-80) cc_final: 0.7633 (m-80) REVERT: C 72 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7160 (tt0) REVERT: C 116 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7204 (mtt90) REVERT: C 134 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8869 (m) REVERT: C 176 MET cc_start: 0.8553 (mmt) cc_final: 0.8122 (mmt) REVERT: C 180 LEU cc_start: 0.9060 (tp) cc_final: 0.8809 (tp) REVERT: C 288 ASP cc_start: 0.7893 (p0) cc_final: 0.7574 (t0) REVERT: D 47 MET cc_start: 0.7199 (mmm) cc_final: 0.6635 (mmt) REVERT: D 49 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: D 99 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: D 116 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7769 (mtp85) REVERT: D 227 MET cc_start: 0.7828 (mmm) cc_final: 0.7569 (tpt) REVERT: E 43 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7639 (p) REVERT: E 44 MET cc_start: 0.8193 (mmt) cc_final: 0.6653 (mpp) REVERT: E 142 LEU cc_start: 0.9325 (tp) cc_final: 0.8897 (mp) outliers start: 68 outliers final: 47 residues processed: 177 average time/residue: 0.2263 time to fit residues: 63.6400 Evaluate side-chains 174 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 117 time to evaluate : 1.628 ------------------------------------------------------------------------------- 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 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 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 351 THR 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 260 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 325 MET 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 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 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 267 ILE 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 172 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 0.0050 chunk 150 optimal weight: 0.0970 chunk 99 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14845 Z= 0.137 Angle : 0.576 10.806 20146 Z= 0.274 Chirality : 0.043 0.143 2242 Planarity : 0.003 0.036 2574 Dihedral : 6.833 59.118 2102 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.42 % Allowed : 17.37 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1840 helix: -0.11 (0.21), residues: 680 sheet: -1.87 (0.31), residues: 285 loop : -1.00 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 356 HIS 0.005 0.000 HIS A 87 PHE 0.016 0.001 PHE B 352 TYR 0.007 0.001 TYR B 166 ARG 0.002 0.000 ARG D 256 *********************** 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 186 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 133 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: A 82 MET cc_start: 0.8313 (tpp) cc_final: 0.8052 (tpt) REVERT: A 124 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8195 (m-10) REVERT: B 123 MET cc_start: 0.8257 (mmm) cc_final: 0.8007 (tmm) REVERT: B 224 GLU cc_start: 0.7799 (tp30) cc_final: 0.7504 (tp30) REVERT: B 313 MET cc_start: 0.8018 (mtp) cc_final: 0.7812 (mtp) REVERT: C 134 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8876 (m) REVERT: C 180 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8756 (tp) REVERT: C 288 ASP cc_start: 0.7849 (p0) cc_final: 0.7515 (t0) REVERT: D 47 MET cc_start: 0.7174 (mmm) cc_final: 0.6600 (mmt) REVERT: D 49 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: D 191 LYS cc_start: 0.9007 (tmtt) cc_final: 0.8442 (ttmt) REVERT: D 227 MET cc_start: 0.7877 (mmm) cc_final: 0.7660 (tpt) REVERT: E 43 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7563 (p) REVERT: E 44 MET cc_start: 0.8147 (mmt) cc_final: 0.6595 (mpp) REVERT: E 132 MET cc_start: 0.8306 (ppp) cc_final: 0.8022 (ppp) REVERT: E 142 LEU cc_start: 0.9299 (tp) cc_final: 0.8854 (mp) REVERT: E 283 MET cc_start: 0.8472 (mmt) cc_final: 0.8232 (mmm) outliers start: 53 outliers final: 38 residues processed: 173 average time/residue: 0.2187 time to fit residues: 60.9032 Evaluate side-chains 164 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 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 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 180 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 49 GLN 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 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 34 ILE 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 267 ILE Chi-restraints excluded: chain E residue 293 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 71 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14845 Z= 0.198 Angle : 0.608 15.629 20146 Z= 0.285 Chirality : 0.044 0.147 2242 Planarity : 0.003 0.032 2574 Dihedral : 6.475 58.351 2093 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.49 % Allowed : 17.88 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.20), residues: 1840 helix: -0.07 (0.21), residues: 680 sheet: -1.85 (0.32), residues: 285 loop : -0.94 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 340 HIS 0.005 0.001 HIS C 87 PHE 0.024 0.001 PHE B 352 TYR 0.008 0.001 TYR B 143 ARG 0.003 0.000 ARG E 147 *********************** 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 175 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 121 time to evaluate : 1.963 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: A 82 MET cc_start: 0.8381 (tpp) cc_final: 0.7999 (tpp) REVERT: A 124 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.8180 (m-10) REVERT: A 337 TYR cc_start: 0.8149 (m-80) cc_final: 0.7759 (m-80) REVERT: B 123 MET cc_start: 0.8314 (mmm) cc_final: 0.8066 (mmm) REVERT: C 116 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7599 (mtt90) REVERT: C 134 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8812 (m) REVERT: C 176 MET cc_start: 0.8437 (mmt) cc_final: 0.8030 (mmt) REVERT: C 288 ASP cc_start: 0.7804 (p0) cc_final: 0.7531 (t0) REVERT: D 47 MET cc_start: 0.7117 (mmm) cc_final: 0.6570 (mmt) REVERT: D 49 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: D 99 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: D 116 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7778 (mtp85) REVERT: D 191 LYS cc_start: 0.9020 (tmtt) cc_final: 0.8510 (ttmt) REVERT: D 227 MET cc_start: 0.7850 (mmm) cc_final: 0.7608 (tpt) REVERT: E 43 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7573 (p) REVERT: E 44 MET cc_start: 0.8160 (mmt) cc_final: 0.6591 (mpp) REVERT: E 132 MET cc_start: 0.8321 (ppp) cc_final: 0.8054 (ppp) REVERT: E 142 LEU cc_start: 0.9343 (tp) cc_final: 0.8796 (mp) REVERT: E 289 ILE cc_start: 0.9233 (mt) cc_final: 0.8922 (tt) outliers start: 54 outliers final: 39 residues processed: 163 average time/residue: 0.2308 time to fit residues: 59.8169 Evaluate side-chains 166 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 1.558 ------------------------------------------------------------------------------- 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 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 325 MET 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 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 257 CYS Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 293 LEU 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 170 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 GLN E 78 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14845 Z= 0.159 Angle : 0.594 15.171 20146 Z= 0.277 Chirality : 0.044 0.157 2242 Planarity : 0.003 0.032 2574 Dihedral : 6.242 58.910 2093 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.10 % Allowed : 17.69 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.20), residues: 1840 helix: 0.01 (0.21), residues: 680 sheet: -1.82 (0.31), residues: 285 loop : -0.82 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 356 HIS 0.004 0.000 HIS C 87 PHE 0.048 0.001 PHE B 352 TYR 0.007 0.001 TYR B 143 ARG 0.002 0.000 ARG A 177 *********************** 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 172 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 1.831 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7909 (tp30) REVERT: A 82 MET cc_start: 0.8341 (tpp) cc_final: 0.8055 (tpt) REVERT: A 124 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.8165 (m-10) REVERT: A 337 TYR cc_start: 0.8066 (m-80) cc_final: 0.7737 (m-80) REVERT: B 123 MET cc_start: 0.8306 (mmm) cc_final: 0.8051 (mmm) REVERT: C 72 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7036 (tt0) REVERT: C 134 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8875 (m) REVERT: C 288 ASP cc_start: 0.7752 (p0) cc_final: 0.7516 (t0) REVERT: D 47 MET cc_start: 0.7115 (mmm) cc_final: 0.6830 (mmt) REVERT: D 99 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: D 116 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7754 (mtp85) REVERT: D 191 LYS cc_start: 0.8967 (tmtt) cc_final: 0.8429 (ttmt) REVERT: D 325 MET cc_start: 0.7934 (mmm) cc_final: 0.7580 (tpp) REVERT: E 43 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7750 (p) REVERT: E 44 MET cc_start: 0.8157 (mmt) cc_final: 0.6550 (mpp) REVERT: E 132 MET cc_start: 0.8326 (ppp) cc_final: 0.8047 (ppp) REVERT: E 142 LEU cc_start: 0.9330 (tp) cc_final: 0.8775 (mp) REVERT: E 283 MET cc_start: 0.8469 (mmt) cc_final: 0.8236 (mmm) REVERT: E 289 ILE cc_start: 0.9222 (mt) cc_final: 0.8939 (tt) REVERT: E 355 MET cc_start: 0.8197 (mmm) cc_final: 0.7917 (mmm) outliers start: 48 outliers final: 37 residues processed: 162 average time/residue: 0.2387 time to fit residues: 62.5355 Evaluate side-chains 163 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 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 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 45 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 325 MET Chi-restraints excluded: chain C residue 351 THR 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 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 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 293 LEU 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 175 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 15 optimal weight: 0.0070 chunk 113 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14845 Z= 0.149 Angle : 0.597 14.529 20146 Z= 0.277 Chirality : 0.044 0.166 2242 Planarity : 0.003 0.031 2574 Dihedral : 5.852 59.125 2084 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.16 % Allowed : 17.95 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.20), residues: 1840 helix: 0.06 (0.21), residues: 680 sheet: -1.80 (0.31), residues: 285 loop : -0.73 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 356 HIS 0.005 0.001 HIS C 87 PHE 0.049 0.001 PHE B 352 TYR 0.006 0.001 TYR B 143 ARG 0.003 0.000 ARG A 177 ********************** 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 167 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 118 time to evaluate : 1.671 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8133 (tp30) REVERT: A 82 MET cc_start: 0.8357 (tpp) cc_final: 0.8092 (tpt) REVERT: A 124 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8120 (m-10) REVERT: A 337 TYR cc_start: 0.8022 (m-80) cc_final: 0.7680 (m-80) REVERT: B 123 MET cc_start: 0.8292 (mmm) cc_final: 0.8034 (mmm) REVERT: C 72 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7110 (tt0) REVERT: C 288 ASP cc_start: 0.7751 (p0) cc_final: 0.7502 (t0) REVERT: D 47 MET cc_start: 0.7101 (mmm) cc_final: 0.6834 (mmt) REVERT: D 99 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: D 116 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7730 (mtp85) REVERT: D 191 LYS cc_start: 0.8959 (tmtt) cc_final: 0.8410 (ttmt) REVERT: E 43 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7726 (p) REVERT: E 44 MET cc_start: 0.8194 (mmt) cc_final: 0.6531 (mpp) REVERT: E 132 MET cc_start: 0.8340 (ppp) cc_final: 0.8056 (ppp) REVERT: E 142 LEU cc_start: 0.9366 (tp) cc_final: 0.8835 (mp) REVERT: E 283 MET cc_start: 0.8447 (mmt) cc_final: 0.8232 (mmm) REVERT: E 289 ILE cc_start: 0.9219 (mt) cc_final: 0.8929 (tt) REVERT: E 355 MET cc_start: 0.8179 (mmm) cc_final: 0.7911 (mmm) outliers start: 49 outliers final: 39 residues processed: 156 average time/residue: 0.2264 time to fit residues: 56.0788 Evaluate side-chains 160 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 1.762 ------------------------------------------------------------------------------- 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 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 132 MET 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 325 MET Chi-restraints excluded: chain C residue 351 THR 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 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 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 293 LEU 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 156 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** 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 = 0.2978 r_free = 0.2978 target = 0.075181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.065387 restraints weight = 33572.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.067101 restraints weight = 18941.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.068255 restraints weight = 12279.247| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14845 Z= 0.205 Angle : 0.616 13.936 20146 Z= 0.287 Chirality : 0.045 0.171 2242 Planarity : 0.004 0.053 2574 Dihedral : 5.903 59.405 2083 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.91 % Allowed : 18.08 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.20), residues: 1840 helix: 0.07 (0.21), residues: 680 sheet: -1.79 (0.31), residues: 285 loop : -0.75 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 356 HIS 0.005 0.001 HIS C 87 PHE 0.050 0.001 PHE B 352 TYR 0.007 0.001 TYR D 279 ARG 0.007 0.000 ARG C 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2485.58 seconds wall clock time: 47 minutes 9.79 seconds (2829.79 seconds total)