Starting phenix.real_space_refine on Fri May 16 15:25:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bt7_30171/05_2025/7bt7_30171.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bt7_30171/05_2025/7bt7_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_30171/05_2025/7bt7_30171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bt7_30171/05_2025/7bt7_30171.map" model { file = "/net/cci-nas-00/data/ceres_data/7bt7_30171/05_2025/7bt7_30171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bt7_30171/05_2025/7bt7_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.09, per 1000 atoms: 0.63 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: 3.62 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: 2.37 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: 4.83 Time building geometry restraints manager: 4.11 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: 3.270 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 36.430 Find NCS groups from input model: 0.750 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14845 Z= 0.198 Angle : 0.662 8.810 20146 Z= 0.360 Chirality : 0.045 0.152 2242 Planarity : 0.004 0.040 2574 Dihedral : 13.362 91.540 5519 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.49 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 Details of bonding type rmsd hydrogen bonds : bond 0.16510 ( 517) hydrogen bonds : angle 6.87554 ( 1395) covalent geometry : bond 0.00436 (14845) covalent geometry : angle 0.66172 (20146) *********************** 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 : 1.698 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: 0.2339 time to fit residues: 106.1220 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 : 1.536 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.072552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.062087 restraints weight = 33762.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.063932 restraints weight = 18253.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.065210 restraints weight = 11650.445| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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= 0.150 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 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 517) hydrogen bonds : angle 5.42055 ( 1395) covalent geometry : bond 0.00342 (14845) covalent geometry : angle 0.63727 (20146) *********************** 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 : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8055 (tp30) REVERT: A 80 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7317 (p0) REVERT: A 82 MET cc_start: 0.8478 (tpp) cc_final: 0.8130 (tpt) REVERT: A 101 HIS cc_start: 0.8931 (m-70) cc_final: 0.8648 (m90) REVERT: A 123 MET cc_start: 0.9036 (mmt) cc_final: 0.8827 (mmm) REVERT: A 143 TYR cc_start: 0.8571 (m-10) cc_final: 0.8369 (m-10) REVERT: A 180 LEU cc_start: 0.8913 (tp) cc_final: 0.8631 (tp) REVERT: A 337 TYR cc_start: 0.8041 (m-80) cc_final: 0.7814 (m-80) REVERT: B 167 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: B 195 GLU cc_start: 0.7817 (pt0) cc_final: 0.7458 (pt0) REVERT: B 313 MET cc_start: 0.8459 (tpp) cc_final: 0.7984 (mtp) REVERT: C 12 ASN cc_start: 0.8650 (t0) cc_final: 0.8024 (p0) REVERT: C 16 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9150 (mt) REVERT: C 72 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: C 116 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7493 (mtt90) REVERT: C 134 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8878 (m) REVERT: C 180 LEU cc_start: 0.9172 (tp) cc_final: 0.8903 (tp) REVERT: C 288 ASP cc_start: 0.7871 (p0) cc_final: 0.7439 (t0) REVERT: D 47 MET cc_start: 0.7258 (mmm) cc_final: 0.6715 (mmt) REVERT: D 49 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: D 116 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7724 (mtp85) REVERT: D 191 LYS cc_start: 0.9208 (tmtt) cc_final: 0.8605 (ttmt) REVERT: D 218 TYR cc_start: 0.9236 (OUTLIER) cc_final: 0.8730 (p90) REVERT: D 227 MET cc_start: 0.8090 (mmm) cc_final: 0.7874 (tpt) REVERT: E 43 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7794 (p) REVERT: E 44 MET cc_start: 0.8175 (mmt) cc_final: 0.6857 (mpp) REVERT: E 142 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8950 (mp) REVERT: E 152 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8924 (t) REVERT: E 162 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.7876 (m110) outliers start: 94 outliers final: 51 residues processed: 213 average time/residue: 0.2127 time to fit residues: 72.3294 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 : 1.629 ------------------------------------------------------------------------------- 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 143 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 167 optimal weight: 0.0470 chunk 94 optimal weight: 4.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.071737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.061427 restraints weight = 34266.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.063252 restraints weight = 18457.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.064487 restraints weight = 11701.490| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1474 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= 0.195 Angle : 0.643 8.009 20146 Z= 0.314 Chirality : 0.047 0.150 2242 Planarity : 0.004 0.035 2574 Dihedral : 9.342 85.957 2146 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % 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: -2.36 (0.19), residues: 1840 helix: -0.87 (0.20), residues: 680 sheet: -2.32 (0.31), residues: 275 loop : -1.80 (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 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 517) hydrogen bonds : angle 5.24167 ( 1395) covalent geometry : bond 0.00455 (14845) covalent geometry : angle 0.64346 (20146) *********************** 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 206 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 116 time to evaluate : 1.561 Fit side-chains REVERT: A 57 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7969 (tp30) REVERT: A 80 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7372 (p0) REVERT: A 82 MET cc_start: 0.8491 (tpp) cc_final: 0.8111 (tpt) REVERT: A 101 HIS cc_start: 0.8964 (m-70) cc_final: 0.8682 (m90) REVERT: A 180 LEU cc_start: 0.8990 (tp) cc_final: 0.8770 (tp) REVERT: A 337 TYR cc_start: 0.8066 (m-80) cc_final: 0.7672 (m-80) REVERT: B 167 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: B 313 MET cc_start: 0.8501 (tpp) cc_final: 0.8081 (mtp) REVERT: C 12 ASN cc_start: 0.8769 (t0) cc_final: 0.7841 (p0) REVERT: C 16 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9143 (mt) REVERT: C 72 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: C 116 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7470 (mtt90) REVERT: C 134 VAL cc_start: 0.9173 (OUTLIER) cc_final: 0.8883 (m) REVERT: C 180 LEU cc_start: 0.9195 (tp) cc_final: 0.8893 (tp) REVERT: C 288 ASP cc_start: 0.7911 (p0) cc_final: 0.7496 (t0) REVERT: D 47 MET cc_start: 0.7268 (mmm) cc_final: 0.6694 (mmt) REVERT: D 49 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: D 99 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: D 116 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7756 (mtp85) REVERT: D 191 LYS cc_start: 0.9149 (tmtt) cc_final: 0.8628 (ttmt) REVERT: D 218 TYR cc_start: 0.9247 (OUTLIER) cc_final: 0.8804 (p90) REVERT: D 227 MET cc_start: 0.7863 (mmm) cc_final: 0.7628 (tpt) REVERT: E 43 VAL cc_start: 0.8171 (OUTLIER) cc_final: 0.7760 (p) REVERT: E 44 MET cc_start: 0.8186 (mmt) cc_final: 0.6863 (mpp) REVERT: E 132 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.8026 (ppp) REVERT: E 142 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8953 (mp) outliers start: 90 outliers final: 56 residues processed: 190 average time/residue: 0.2106 time to fit residues: 63.7340 Evaluate side-chains 182 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 112 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 89 THR 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 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 132 MET Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 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 108 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 115 optimal weight: 0.0010 chunk 59 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.074060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.064318 restraints weight = 33712.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.066015 restraints weight = 18962.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.067155 restraints weight = 12289.602| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14845 Z= 0.110 Angle : 0.591 10.845 20146 Z= 0.285 Chirality : 0.044 0.144 2242 Planarity : 0.004 0.036 2574 Dihedral : 8.703 78.119 2136 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.65 % Allowed : 15.11 % Favored : 80.25 % 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: -1.95 (0.20), residues: 1840 helix: -0.54 (0.21), residues: 680 sheet: -2.17 (0.31), residues: 285 loop : -1.51 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 340 HIS 0.004 0.000 HIS C 87 PHE 0.013 0.001 PHE B 352 TYR 0.008 0.001 TYR D 166 ARG 0.002 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.02906 ( 517) hydrogen bonds : angle 4.94787 ( 1395) covalent geometry : bond 0.00249 (14845) covalent geometry : angle 0.59128 (20146) *********************** 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 204 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 132 time to evaluate : 1.710 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: 0.8358 (OUTLIER) cc_final: 0.7954 (tp30) REVERT: A 80 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7306 (p0) REVERT: A 82 MET cc_start: 0.8345 (tpp) cc_final: 0.7942 (tpt) REVERT: A 101 HIS cc_start: 0.8788 (m-70) cc_final: 0.8565 (m90) REVERT: A 123 MET cc_start: 0.8734 (mmm) cc_final: 0.8414 (mmm) REVERT: A 180 LEU cc_start: 0.8829 (tp) cc_final: 0.8532 (tp) REVERT: A 337 TYR cc_start: 0.7944 (m-80) cc_final: 0.7658 (m-80) REVERT: B 283 MET cc_start: 0.8590 (mmm) cc_final: 0.8142 (mmt) REVERT: C 16 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9147 (mt) REVERT: C 116 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7275 (mtt90) REVERT: C 134 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8887 (m) REVERT: C 176 MET cc_start: 0.8511 (mmt) cc_final: 0.8165 (mmt) REVERT: C 180 LEU cc_start: 0.9106 (tp) cc_final: 0.8891 (tp) REVERT: C 288 ASP cc_start: 0.7804 (p0) cc_final: 0.7488 (t0) REVERT: D 47 MET cc_start: 0.7145 (mmm) cc_final: 0.6606 (mmt) REVERT: D 49 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: D 99 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: D 116 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7690 (mtp85) REVERT: D 191 LYS cc_start: 0.9072 (tmtt) cc_final: 0.8591 (ttmt) REVERT: D 227 MET cc_start: 0.7836 (mmm) cc_final: 0.7571 (tpt) REVERT: E 43 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7723 (p) REVERT: E 44 MET cc_start: 0.8109 (mmt) cc_final: 0.6800 (mpp) REVERT: E 142 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8861 (mp) outliers start: 72 outliers final: 42 residues processed: 187 average time/residue: 0.2155 time to fit residues: 64.0370 Evaluate side-chains 169 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 116 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 89 THR 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 182 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.073202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.063430 restraints weight = 34189.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.065112 restraints weight = 19250.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.066254 restraints weight = 12513.725| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14845 Z= 0.152 Angle : 0.609 9.076 20146 Z= 0.293 Chirality : 0.045 0.146 2242 Planarity : 0.004 0.035 2574 Dihedral : 8.277 74.908 2118 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.84 % Allowed : 15.43 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.71 (0.20), residues: 1840 helix: -0.42 (0.21), residues: 680 sheet: -1.95 (0.32), residues: 275 loop : -1.34 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 340 HIS 0.005 0.001 HIS C 87 PHE 0.012 0.001 PHE B 352 TYR 0.012 0.001 TYR B 166 ARG 0.003 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 517) hydrogen bonds : angle 4.93261 ( 1395) covalent geometry : bond 0.00356 (14845) covalent geometry : angle 0.60945 (20146) *********************** 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 194 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 119 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8917 (mt) REVERT: A 57 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7949 (tp30) REVERT: A 80 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7332 (p0) REVERT: A 82 MET cc_start: 0.8407 (tpp) cc_final: 0.8048 (tpt) REVERT: A 101 HIS cc_start: 0.8846 (m-70) cc_final: 0.8627 (m90) REVERT: A 180 LEU cc_start: 0.8833 (tp) cc_final: 0.8518 (tp) REVERT: A 337 TYR cc_start: 0.7962 (m-80) cc_final: 0.7664 (m-80) REVERT: B 10 CYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8666 (p) REVERT: B 313 MET cc_start: 0.8119 (ttm) cc_final: 0.7822 (mtp) REVERT: C 72 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7122 (tt0) REVERT: C 116 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7261 (mtt90) REVERT: C 134 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8859 (m) REVERT: C 176 MET cc_start: 0.8505 (mmt) cc_final: 0.8118 (mmt) REVERT: C 180 LEU cc_start: 0.9117 (tp) cc_final: 0.8897 (tp) REVERT: C 288 ASP cc_start: 0.7829 (p0) cc_final: 0.7509 (t0) REVERT: D 47 MET cc_start: 0.7173 (mmm) cc_final: 0.6617 (mmt) REVERT: D 49 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: D 99 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: D 116 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7724 (mtp85) REVERT: D 191 LYS cc_start: 0.9082 (tmtt) cc_final: 0.8646 (ttmt) REVERT: D 227 MET cc_start: 0.7838 (mmm) cc_final: 0.7565 (tpt) REVERT: E 43 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7711 (p) REVERT: E 44 MET cc_start: 0.8143 (mmt) cc_final: 0.6844 (mpp) REVERT: E 142 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8907 (mp) outliers start: 75 outliers final: 52 residues processed: 181 average time/residue: 0.2264 time to fit residues: 65.6305 Evaluate side-chains 179 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 115 time to evaluate : 1.953 ------------------------------------------------------------------------------- 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 89 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 358 THR 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 152 VAL 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 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 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 103 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 54 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 180 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN E 78 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.073363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.063595 restraints weight = 34166.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.065275 restraints weight = 19287.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.066417 restraints weight = 12570.691| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14845 Z= 0.147 Angle : 0.603 9.648 20146 Z= 0.289 Chirality : 0.045 0.149 2242 Planarity : 0.003 0.035 2574 Dihedral : 7.967 70.128 2114 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.84 % Allowed : 15.82 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.59 (0.20), residues: 1840 helix: -0.36 (0.21), residues: 680 sheet: -1.90 (0.33), residues: 275 loop : -1.24 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 340 HIS 0.005 0.001 HIS C 87 PHE 0.017 0.001 PHE B 352 TYR 0.011 0.001 TYR B 166 ARG 0.002 0.000 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.02920 ( 517) hydrogen bonds : angle 4.85750 ( 1395) covalent geometry : bond 0.00345 (14845) covalent geometry : angle 0.60302 (20146) *********************** 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 193 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 118 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8874 (mt) REVERT: A 47 MET cc_start: 0.7464 (mmm) cc_final: 0.7201 (mmm) REVERT: A 57 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7960 (tp30) REVERT: A 80 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7353 (p0) REVERT: A 82 MET cc_start: 0.8363 (tpp) cc_final: 0.7930 (tpp) REVERT: A 180 LEU cc_start: 0.8785 (tp) cc_final: 0.8423 (tp) REVERT: A 337 TYR cc_start: 0.7899 (m-80) cc_final: 0.7561 (m-80) REVERT: B 313 MET cc_start: 0.8088 (ttm) cc_final: 0.7786 (mtp) REVERT: C 72 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7112 (tt0) REVERT: C 116 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7232 (mtt90) REVERT: C 134 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8895 (m) REVERT: C 180 LEU cc_start: 0.9059 (tp) cc_final: 0.8848 (tp) REVERT: C 288 ASP cc_start: 0.7797 (p0) cc_final: 0.7514 (t0) REVERT: D 47 MET cc_start: 0.7144 (mmm) cc_final: 0.6585 (mmt) REVERT: D 49 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: D 99 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: D 116 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7753 (mtp85) REVERT: D 227 MET cc_start: 0.7837 (mmm) cc_final: 0.7566 (tpt) REVERT: E 43 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7708 (p) REVERT: E 44 MET cc_start: 0.8147 (mmt) cc_final: 0.6786 (mpp) REVERT: E 142 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8880 (mp) outliers start: 75 outliers final: 52 residues processed: 181 average time/residue: 0.2054 time to fit residues: 59.5231 Evaluate side-chains 179 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 116 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 34 ILE 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 179 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 338 SER 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 186 THR 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 134 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 127 optimal weight: 0.7980 chunk 143 optimal weight: 0.4980 chunk 75 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 4 optimal weight: 0.0670 chunk 104 optimal weight: 4.9990 chunk 56 optimal weight: 0.0570 chunk 110 optimal weight: 0.7980 overall best weight: 0.4236 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.076288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.066588 restraints weight = 33520.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.068329 restraints weight = 18617.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.069475 restraints weight = 11978.895| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14845 Z= 0.090 Angle : 0.579 10.430 20146 Z= 0.277 Chirality : 0.043 0.144 2242 Planarity : 0.003 0.034 2574 Dihedral : 7.259 61.405 2111 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.29 % Allowed : 17.75 % Favored : 78.95 % 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: -1.40 (0.20), residues: 1840 helix: -0.15 (0.21), residues: 680 sheet: -1.95 (0.31), residues: 285 loop : -1.09 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 356 HIS 0.004 0.001 HIS C 87 PHE 0.017 0.001 PHE B 352 TYR 0.011 0.001 TYR B 166 ARG 0.004 0.000 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.02534 ( 517) hydrogen bonds : angle 4.69053 ( 1395) covalent geometry : bond 0.00199 (14845) covalent geometry : angle 0.57918 (20146) *********************** 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 194 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 1.651 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7402 (mmm) cc_final: 0.7169 (mmm) REVERT: A 57 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7933 (tp30) REVERT: A 82 MET cc_start: 0.8254 (tpp) cc_final: 0.7970 (tpt) REVERT: A 124 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8174 (m-10) REVERT: A 337 TYR cc_start: 0.7838 (m-80) cc_final: 0.7512 (m-80) REVERT: B 54 VAL cc_start: 0.9644 (OUTLIER) cc_final: 0.9405 (m) REVERT: B 123 MET cc_start: 0.8218 (mmm) cc_final: 0.7987 (tmm) REVERT: B 224 GLU cc_start: 0.7746 (tp30) cc_final: 0.7469 (tp30) REVERT: B 299 MET cc_start: 0.6667 (mtp) cc_final: 0.6463 (mtt) REVERT: C 103 THR cc_start: 0.9235 (m) cc_final: 0.9025 (p) REVERT: C 288 ASP cc_start: 0.7780 (p0) cc_final: 0.7463 (t0) REVERT: D 47 MET cc_start: 0.7108 (mmm) cc_final: 0.6554 (mmt) REVERT: D 49 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: D 191 LYS cc_start: 0.8975 (tmtt) cc_final: 0.8414 (ttmt) REVERT: E 43 VAL cc_start: 0.8074 (OUTLIER) cc_final: 0.7623 (p) REVERT: E 44 MET cc_start: 0.8071 (mmt) cc_final: 0.6639 (mpp) REVERT: E 142 LEU cc_start: 0.9275 (tp) cc_final: 0.8926 (mp) REVERT: E 154 ASP cc_start: 0.8114 (t0) cc_final: 0.7890 (t0) REVERT: E 217 CYS cc_start: 0.9051 (m) cc_final: 0.8350 (m) outliers start: 51 outliers final: 32 residues processed: 182 average time/residue: 0.1968 time to fit residues: 58.0386 Evaluate side-chains 161 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS 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 124 PHE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain B residue 16 LEU 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 142 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain 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 267 ILE 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 63 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 134 optimal weight: 0.0010 chunk 118 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.073723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.064015 restraints weight = 33834.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.065633 restraints weight = 19119.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.066766 restraints weight = 12652.616| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14845 Z= 0.167 Angle : 0.638 14.422 20146 Z= 0.300 Chirality : 0.046 0.188 2242 Planarity : 0.004 0.050 2574 Dihedral : 6.700 62.855 2092 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.36 % Allowed : 17.95 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.36 (0.20), residues: 1840 helix: -0.12 (0.21), residues: 680 sheet: -1.94 (0.32), residues: 285 loop : -1.07 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 340 HIS 0.008 0.001 HIS A 87 PHE 0.024 0.001 PHE B 352 TYR 0.008 0.001 TYR B 166 ARG 0.004 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 517) hydrogen bonds : angle 4.75855 ( 1395) covalent geometry : bond 0.00395 (14845) covalent geometry : angle 0.63752 (20146) *********************** 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 177 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 125 time to evaluate : 1.757 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7509 (mmm) cc_final: 0.7246 (mmm) REVERT: A 57 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7882 (tp30) REVERT: A 82 MET cc_start: 0.8412 (tpp) cc_final: 0.8017 (tpp) REVERT: B 123 MET cc_start: 0.8273 (mmm) cc_final: 0.8005 (mmm) REVERT: B 224 GLU cc_start: 0.7726 (tp30) cc_final: 0.7475 (tp30) REVERT: C 103 THR cc_start: 0.9273 (m) cc_final: 0.9053 (p) REVERT: D 47 MET cc_start: 0.7118 (mmm) cc_final: 0.6564 (mmt) REVERT: D 49 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: D 191 LYS cc_start: 0.9021 (tmtt) cc_final: 0.8494 (ttmt) REVERT: E 43 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7641 (p) REVERT: E 44 MET cc_start: 0.8086 (mmt) cc_final: 0.6633 (mpp) REVERT: E 142 LEU cc_start: 0.9351 (tp) cc_final: 0.8836 (mp) outliers start: 52 outliers final: 43 residues processed: 166 average time/residue: 0.2119 time to fit residues: 57.3741 Evaluate side-chains 167 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 34 ILE 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 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 143 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 229 THR 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 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 132 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 370 VAL 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 175 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain 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 370 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.6706 > 50: distance: 117 - 122: 11.818 distance: 122 - 123: 24.760 distance: 123 - 124: 19.581 distance: 123 - 126: 13.645 distance: 124 - 125: 25.924 distance: 124 - 133: 38.632 distance: 126 - 127: 26.056 distance: 127 - 128: 14.019 distance: 128 - 129: 15.124 distance: 129 - 130: 5.867 distance: 130 - 131: 9.650 distance: 130 - 132: 17.153 distance: 133 - 134: 5.778 distance: 134 - 135: 18.545 distance: 134 - 137: 14.058 distance: 135 - 136: 12.034 distance: 135 - 144: 10.947 distance: 137 - 138: 9.783 distance: 138 - 139: 11.581 distance: 138 - 140: 12.848 distance: 139 - 141: 5.468 distance: 140 - 142: 3.775 distance: 141 - 143: 7.954 distance: 142 - 143: 9.264 distance: 144 - 145: 10.567 distance: 145 - 146: 4.168 distance: 145 - 148: 7.432 distance: 146 - 155: 4.624 distance: 148 - 149: 10.761 distance: 149 - 150: 10.777 distance: 150 - 151: 16.507 distance: 151 - 152: 7.828 distance: 152 - 153: 7.509 distance: 152 - 154: 9.590 distance: 155 - 156: 5.333 distance: 156 - 157: 12.826 distance: 156 - 159: 3.443 distance: 157 - 158: 13.420 distance: 157 - 161: 9.156 distance: 159 - 160: 15.096 distance: 161 - 162: 4.904 distance: 161 - 167: 5.199 distance: 162 - 163: 11.555 distance: 162 - 165: 7.607 distance: 163 - 164: 7.640 distance: 163 - 168: 16.765 distance: 165 - 166: 11.458 distance: 166 - 167: 7.099 distance: 168 - 169: 9.269 distance: 169 - 170: 5.737 distance: 169 - 172: 7.995 distance: 170 - 171: 8.289 distance: 170 - 177: 7.008 distance: 172 - 173: 9.303 distance: 173 - 174: 4.223 distance: 174 - 175: 14.676 distance: 174 - 176: 5.958 distance: 177 - 178: 5.991 distance: 178 - 179: 6.108 distance: 178 - 181: 11.564 distance: 179 - 184: 7.252 distance: 181 - 182: 6.660 distance: 181 - 183: 3.490 distance: 184 - 185: 6.856 distance: 186 - 187: 4.583 distance: 186 - 192: 9.425 distance: 188 - 189: 7.184 distance: 189 - 190: 12.455 distance: 189 - 191: 13.299 distance: 192 - 193: 5.893 distance: 193 - 194: 4.100 distance: 193 - 196: 8.095 distance: 194 - 195: 9.948 distance: 194 - 203: 11.622 distance: 196 - 197: 5.735 distance: 197 - 198: 4.915 distance: 197 - 199: 8.354 distance: 198 - 200: 7.383 distance: 199 - 201: 12.309 distance: 200 - 202: 13.574 distance: 201 - 202: 13.535 distance: 203 - 204: 6.817 distance: 204 - 205: 9.273 distance: 204 - 207: 5.430 distance: 205 - 212: 5.471 distance: 207 - 208: 11.866 distance: 208 - 209: 6.352 distance: 209 - 210: 6.398 distance: 209 - 211: 7.435