Starting phenix.real_space_refine on Thu Aug 6 21:07:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e2l_27842/08_2026/8e2l_27842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2l_27842/08_2026/8e2l_27842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e2l_27842/08_2026/8e2l_27842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2l_27842/08_2026/8e2l_27842.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8e2l_27842/08_2026/8e2l_27842.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e2l_27842/08_2026/8e2l_27842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e2l_27842/08_2026/8e2l_27842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2l_27842/08_2026/8e2l_27842.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.048 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 27 5.49 5 Mg 5 5.21 5 S 54 5.16 5 C 10698 2.51 5 N 3027 2.21 5 O 3281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17092 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3122 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 7, 'GLN:plan1': 5, 'PHE:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 12, 'TRP:plan': 2, 'TYR:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 260 Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3114 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 7, 'GLN:plan1': 5, 'PHE:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 12, 'TRP:plan': 2, 'TYR:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 260 Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3122 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 7, 'GLN:plan1': 5, 'PHE:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 12, 'TRP:plan': 2, 'TYR:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 260 Chain: "D" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3122 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 7, 'GLN:plan1': 5, 'PHE:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 12, 'TRP:plan': 2, 'TYR:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 260 Chain: "E" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2145 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2067 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain breaks: 2 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.68, per 1000 atoms: 0.22 Number of scatterers: 17092 At special positions: 0 Unit cell: (100.58, 167.99, 188.32, 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 54 16.00 P 27 15.00 Mg 5 11.99 O 3281 8.00 N 3027 7.00 C 10698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 723.4 milliseconds 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4444 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 19 sheets defined 39.1% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.632A pdb=" N ALA C 52 " --> pdb=" O GLU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.728A pdb=" N THR C 106 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 155 Processing helix chain 'C' and resid 174 through 180 Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 219 through 226 Processing helix chain 'C' and resid 228 through 235 Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 263 through 268 removed outlier: 4.048A pdb=" N ALA C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 300 through 314 removed outlier: 3.522A pdb=" N ILE C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 341 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 373 through 389 removed outlier: 3.605A pdb=" N VAL C 377 " --> pdb=" O ASN C 373 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 378 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 403 removed outlier: 3.569A pdb=" N MET C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 430 Processing helix chain 'C' and resid 457 through 462 Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.685A pdb=" N THR A 106 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 174 through 181 removed outlier: 4.380A pdb=" N PHE A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 removed outlier: 3.778A pdb=" N ARG A 203 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 300 through 314 removed outlier: 3.717A pdb=" N ILE A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 340 Processing helix chain 'A' and resid 350 through 360 removed outlier: 4.633A pdb=" N GLU A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 389 removed outlier: 4.217A pdb=" N ASP A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 removed outlier: 3.771A pdb=" N MET A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.685A pdb=" N THR B 106 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 174 through 181 removed outlier: 4.380A pdb=" N PHE B 181 " --> pdb=" O TYR B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 removed outlier: 3.778A pdb=" N ARG B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 226 Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 249 through 252 Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.519A pdb=" N VAL B 267 " --> pdb=" O ASN B 263 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 263 through 268' Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 300 through 314 removed outlier: 3.501A pdb=" N ILE B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 350 through 360 removed outlier: 4.181A pdb=" N GLU B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 389 removed outlier: 3.574A pdb=" N VAL B 377 " --> pdb=" O ASN B 373 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 403 removed outlier: 3.690A pdb=" N MET B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 430 Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'D' and resid 66 through 73 removed outlier: 3.836A pdb=" N LYS D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.720A pdb=" N THR D 106 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 174 through 181 removed outlier: 4.084A pdb=" N PHE D 181 " --> pdb=" O TYR D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 219 through 226 Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 253 through 263 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.502A pdb=" N VAL D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 263 through 268' Processing helix chain 'D' and resid 276 through 280 Processing helix chain 'D' and resid 300 through 314 removed outlier: 3.514A pdb=" N ILE D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 341 Processing helix chain 'D' and resid 350 through 360 removed outlier: 4.113A pdb=" N GLU D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 389 removed outlier: 3.540A pdb=" N VAL D 377 " --> pdb=" O ASN D 373 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP D 379 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 413 through 430 Processing helix chain 'D' and resid 457 through 463 Processing helix chain 'E' and resid 249 through 263 removed outlier: 4.025A pdb=" N LEU E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP E 256 " --> pdb=" O GLN E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 268 removed outlier: 4.006A pdb=" N ALA E 268 " --> pdb=" O THR E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 Processing helix chain 'E' and resid 300 through 314 removed outlier: 3.525A pdb=" N ILE E 314 " --> pdb=" O LEU E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 341 Processing helix chain 'E' and resid 350 through 360 removed outlier: 4.167A pdb=" N GLU E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 389 removed outlier: 3.550A pdb=" N VAL E 377 " --> pdb=" O ASN E 373 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR E 380 " --> pdb=" O THR E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 413 through 430 Processing helix chain 'E' and resid 449 through 453 removed outlier: 4.215A pdb=" N ILE E 453 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 462 Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 276 through 281 Processing helix chain 'F' and resid 300 through 314 removed outlier: 3.519A pdb=" N ILE F 314 " --> pdb=" O LEU F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 341 Processing helix chain 'F' and resid 343 through 349 removed outlier: 3.571A pdb=" N GLU F 346 " --> pdb=" O ARG F 343 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU F 348 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU F 349 " --> pdb=" O GLU F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 360 removed outlier: 4.218A pdb=" N GLU F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 389 removed outlier: 3.609A pdb=" N VAL F 377 " --> pdb=" O ASN F 373 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP F 379 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR F 380 " --> pdb=" O THR F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 403 removed outlier: 3.669A pdb=" N MET F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 430 Processing helix chain 'F' and resid 457 through 462 Processing sheet with id=AA1, first strand: chain 'C' and resid 160 through 161 removed outlier: 6.397A pdb=" N VAL C 141 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL C 184 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 290 through 293 removed outlier: 3.631A pdb=" N ILE C 436 " --> pdb=" O ILE C 395 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 465 through 470 removed outlier: 6.839A pdb=" N VAL C 466 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR C 486 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 483 " --> pdb=" O PHE C 497 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 501 through 502 removed outlier: 3.513A pdb=" N THR C 507 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 161 removed outlier: 3.902A pdb=" N VAL A 161 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL A 140 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 246 through 247 removed outlier: 6.647A pdb=" N VAL B 393 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ILE B 436 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 290 through 293 Processing sheet with id=AA8, first strand: chain 'A' and resid 465 through 470 removed outlier: 6.990A pdb=" N VAL A 466 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 486 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 483 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 497 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP A 500 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 160 through 161 removed outlier: 3.903A pdb=" N VAL B 161 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 140 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 465 through 470 removed outlier: 6.875A pdb=" N VAL B 466 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR B 486 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 483 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 497 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP B 500 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 507 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 141 through 142 removed outlier: 3.767A pdb=" N LEU D 142 " --> pdb=" O THR D 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 246 through 248 removed outlier: 6.505A pdb=" N THR E 319 " --> pdb=" O TYR E 364 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N MET E 366 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TRP E 321 " --> pdb=" O MET E 366 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL E 393 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ILE E 436 " --> pdb=" O VAL E 393 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE E 395 " --> pdb=" O ILE E 436 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 290 through 293 Processing sheet with id=AB5, first strand: chain 'D' and resid 465 through 470 removed outlier: 6.885A pdb=" N VAL D 466 " --> pdb=" O THR D 486 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D 483 " --> pdb=" O PHE D 497 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 501 through 502 removed outlier: 3.553A pdb=" N THR D 507 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 465 through 470 removed outlier: 6.901A pdb=" N VAL E 466 " --> pdb=" O THR E 486 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR E 486 " --> pdb=" O VAL E 466 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU E 483 " --> pdb=" O PHE E 497 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE E 497 " --> pdb=" O LEU E 483 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 501 through 502 removed outlier: 3.591A pdb=" N THR E 507 " --> pdb=" O ILE E 502 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 290 through 293 removed outlier: 6.801A pdb=" N VAL F 393 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ILE F 436 " --> pdb=" O VAL F 393 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 468 through 470 removed outlier: 3.705A pdb=" N LEU F 483 " --> pdb=" O PHE F 497 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 497 " --> pdb=" O LEU F 483 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP F 500 " --> pdb=" O SER F 509 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1770 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4895 1.33 - 1.45: 2731 1.45 - 1.57: 9625 1.57 - 1.69: 48 1.69 - 1.81: 90 Bond restraints: 17389 Sorted by residual: bond pdb=" C4 ATP E 601 " pdb=" C5 ATP E 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.63e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.61e+01 bond pdb=" C4 ATP F 601 " pdb=" C5 ATP F 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.56e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.45e+01 bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.41e+01 ... (remaining 17384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 23639 4.03 - 8.05: 68 8.05 - 12.08: 6 12.08 - 16.11: 2 16.11 - 20.13: 8 Bond angle restraints: 23723 Sorted by residual: angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 119.74 20.13 1.00e+00 1.00e+00 4.05e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.77 20.10 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 119.95 19.92 1.00e+00 1.00e+00 3.97e+02 angle pdb=" PB ATP E 601 " pdb=" O3B ATP E 601 " pdb=" PG ATP E 601 " ideal model delta sigma weight residual 139.87 119.97 19.90 1.00e+00 1.00e+00 3.96e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 120.00 19.87 1.00e+00 1.00e+00 3.95e+02 ... (remaining 23718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.41: 9542 23.41 - 46.81: 516 46.81 - 70.22: 109 70.22 - 93.62: 25 93.62 - 117.03: 1 Dihedral angle restraints: 10193 sinusoidal: 3360 harmonic: 6833 Sorted by residual: dihedral pdb=" CA ILE A 240 " pdb=" C ILE A 240 " pdb=" N PRO A 241 " pdb=" CA PRO A 241 " ideal model delta harmonic sigma weight residual -180.00 -62.97 -117.03 0 5.00e+00 4.00e-02 5.48e+02 dihedral pdb=" CA PHE C 250 " pdb=" C PHE C 250 " pdb=" N LYS C 251 " pdb=" CA LYS C 251 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" C ASN B 397 " pdb=" N ASN B 397 " pdb=" CA ASN B 397 " pdb=" CB ASN B 397 " ideal model delta harmonic sigma weight residual -122.60 -133.66 11.06 0 2.50e+00 1.60e-01 1.96e+01 ... (remaining 10190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2507 0.077 - 0.153: 257 0.153 - 0.230: 6 0.230 - 0.306: 4 0.306 - 0.383: 2 Chirality restraints: 2776 Sorted by residual: chirality pdb=" CA ASN B 397 " pdb=" N ASN B 397 " pdb=" C ASN B 397 " pdb=" CB ASN B 397 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CA ASN E 397 " pdb=" N ASN E 397 " pdb=" C ASN E 397 " pdb=" CB ASN E 397 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ASN C 397 " pdb=" N ASN C 397 " pdb=" C ASN C 397 " pdb=" CB ASN C 397 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 2773 not shown) Planarity restraints: 3058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 394 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C ILE B 394 " -0.045 2.00e-02 2.50e+03 pdb=" O ILE B 394 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE B 395 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 237 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C LYS A 237 " 0.043 2.00e-02 2.50e+03 pdb=" O LYS A 237 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 238 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 275 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO A 276 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.031 5.00e-02 4.00e+02 ... (remaining 3055 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 120 2.60 - 3.18: 14832 3.18 - 3.75: 24950 3.75 - 4.33: 32806 4.33 - 4.90: 54251 Nonbonded interactions: 126959 Sorted by model distance: nonbonded pdb=" O1B ATP D 601 " pdb="MG MG D 602 " model vdw 2.028 2.170 nonbonded pdb=" O3G ATP D 601 " pdb="MG MG D 602 " model vdw 2.030 2.170 nonbonded pdb=" OE1 GLN B 325 " pdb="MG MG B 602 " model vdw 2.038 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 2.039 2.170 nonbonded pdb=" O1B ATP E 601 " pdb="MG MG E 602 " model vdw 2.065 2.170 ... (remaining 126954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 48 through 404 or resid 410 through 512)) selection = (chain 'C' and (resid 48 through 404 or resid 410 through 512)) selection = (chain 'D' and (resid 48 through 404 or resid 410 through 512)) } ncs_group { reference = (chain 'E' and (resid 244 through 259 or resid 269 through 602)) selection = chain 'F' } 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: 3.220 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.530 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 0.081 17389 Z= 0.300 Angle : 0.737 20.135 23723 Z= 0.576 Chirality : 0.045 0.383 2776 Planarity : 0.003 0.055 3058 Dihedral : 15.294 117.029 5749 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.78 % Favored : 92.09 % Rotamer: Outliers : 0.42 % Allowed : 0.71 % Favored : 98.87 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.18), residues: 2340 helix: 0.79 (0.20), residues: 803 sheet: 0.22 (0.32), residues: 304 loop : -1.88 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.020 0.001 TYR C 386 PHE 0.023 0.001 PHE B 358 TRP 0.016 0.001 TRP F 272 HIS 0.004 0.001 HIS D 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.30 (17389) covalent geometry : angle 0.73692 / 0.58 (23723) hydrogen bonds : bond 0.21066 / 15.79 ( 622) hydrogen bonds : angle 7.60123 / 5.42 ( 1770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 0.590 Fit side-chains REVERT: C 375 LYS cc_start: 0.9049 (mmpt) cc_final: 0.8822 (tppt) REVERT: C 386 TYR cc_start: 0.8901 (m-80) cc_final: 0.8558 (m-80) REVERT: A 386 TYR cc_start: 0.8718 (m-80) cc_final: 0.8242 (m-80) REVERT: A 438 HIS cc_start: 0.5581 (m90) cc_final: 0.4881 (m-70) REVERT: B 491 ASP cc_start: 0.8427 (m-30) cc_final: 0.8127 (m-30) REVERT: E 464 ASP cc_start: 0.8656 (m-30) cc_final: 0.8285 (m-30) REVERT: F 397 ASN cc_start: 0.8324 (m-40) cc_final: 0.8100 (t0) outliers start: 6 outliers final: 1 residues processed: 151 average time/residue: 0.1303 time to fit residues: 30.8702 Evaluate side-chains 109 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 396 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 40.0000 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 30.0000 chunk 235 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 397 ASN A 392 HIS D 369 HIS E 432 HIS ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.105924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.070353 restraints weight = 50575.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.073056 restraints weight = 21459.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.074749 restraints weight = 13300.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 73)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.075787 restraints weight = 10190.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.076335 restraints weight = 8687.268| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17389 Z= 0.171 Angle : 0.532 13.500 23723 Z= 0.291 Chirality : 0.043 0.249 2776 Planarity : 0.004 0.089 3058 Dihedral : 10.541 89.718 2595 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.74 % Favored : 92.22 % Rotamer: Outliers : 1.06 % Allowed : 7.34 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.18), residues: 2340 helix: 0.91 (0.19), residues: 830 sheet: -0.03 (0.31), residues: 327 loop : -2.01 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 481 TYR 0.021 0.001 TYR A 351 PHE 0.028 0.002 PHE F 358 TRP 0.020 0.002 TRP C 195 HIS 0.010 0.001 HIS D 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (17389) covalent geometry : angle 0.53172 / 0.29 (23723) hydrogen bonds : bond 0.04406 / 3.35 ( 622) hydrogen bonds : angle 5.51436 / 3.95 ( 1770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 402 MET cc_start: 0.8349 (tmm) cc_final: 0.8020 (tmm) REVERT: A 386 TYR cc_start: 0.8650 (m-80) cc_final: 0.8185 (m-80) REVERT: A 402 MET cc_start: 0.7358 (tmm) cc_final: 0.7145 (tmm) REVERT: A 438 HIS cc_start: 0.6279 (m90) cc_final: 0.5438 (m90) REVERT: B 491 ASP cc_start: 0.8365 (m-30) cc_final: 0.8107 (m-30) REVERT: E 464 ASP cc_start: 0.8711 (m-30) cc_final: 0.8371 (m-30) outliers start: 15 outliers final: 8 residues processed: 122 average time/residue: 0.1236 time to fit residues: 24.4071 Evaluate side-chains 113 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 244 HIS Chi-restraints excluded: chain F residue 250 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 233 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 142 optimal weight: 40.0000 chunk 89 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 224 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 432 HIS ** F 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.104264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.068543 restraints weight = 50715.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.071158 restraints weight = 21697.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.072765 restraints weight = 13519.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.073735 restraints weight = 10452.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.074272 restraints weight = 8997.047| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17389 Z= 0.184 Angle : 0.524 12.342 23723 Z= 0.287 Chirality : 0.043 0.219 2776 Planarity : 0.004 0.098 3058 Dihedral : 10.601 89.688 2595 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 1.41 % Allowed : 11.86 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.18), residues: 2340 helix: 0.84 (0.19), residues: 847 sheet: -0.37 (0.31), residues: 310 loop : -2.00 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.016 0.001 TYR C 386 PHE 0.023 0.002 PHE F 358 TRP 0.038 0.002 TRP A 354 HIS 0.010 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (17389) covalent geometry : angle 0.52430 / 0.29 (23723) hydrogen bonds : bond 0.03751 / 2.86 ( 622) hydrogen bonds : angle 5.13133 / 3.67 ( 1770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 402 MET cc_start: 0.7486 (tmm) cc_final: 0.7260 (tmm) REVERT: A 438 HIS cc_start: 0.6124 (m90) cc_final: 0.5164 (m90) REVERT: B 317 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8313 (p) REVERT: B 491 ASP cc_start: 0.8486 (m-30) cc_final: 0.8233 (m-30) REVERT: E 464 ASP cc_start: 0.8664 (m-30) cc_final: 0.8390 (m-30) REVERT: F 397 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7334 (t0) outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 0.1149 time to fit residues: 22.8198 Evaluate side-chains 116 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 431 CYS Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 397 ASN Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 47 optimal weight: 40.0000 chunk 97 optimal weight: 30.0000 chunk 87 optimal weight: 5.9990 chunk 59 optimal weight: 50.0000 chunk 163 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 140 optimal weight: 50.0000 chunk 235 optimal weight: 5.9990 chunk 115 optimal weight: 0.0670 chunk 142 optimal weight: 40.0000 overall best weight: 2.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 263 ASN ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS ** D 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.103252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.067388 restraints weight = 50995.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.069945 restraints weight = 21882.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071539 restraints weight = 13658.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.072499 restraints weight = 10529.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.073087 restraints weight = 9052.258| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17389 Z= 0.198 Angle : 0.528 11.402 23723 Z= 0.287 Chirality : 0.043 0.260 2776 Planarity : 0.003 0.087 3058 Dihedral : 10.578 89.608 2595 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 1.91 % Allowed : 14.48 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.18), residues: 2340 helix: 0.92 (0.19), residues: 845 sheet: -0.73 (0.30), residues: 317 loop : -1.99 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 446 TYR 0.016 0.001 TYR A 388 PHE 0.020 0.002 PHE F 358 TRP 0.038 0.002 TRP A 354 HIS 0.008 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (17389) covalent geometry : angle 0.52836 / 0.29 (23723) hydrogen bonds : bond 0.03539 / 2.70 ( 622) hydrogen bonds : angle 5.00996 / 3.59 ( 1770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.709 Fit side-chains REVERT: C 443 GLU cc_start: 0.6588 (pp20) cc_final: 0.6063 (pp20) REVERT: A 354 TRP cc_start: 0.8999 (OUTLIER) cc_final: 0.8752 (t60) REVERT: A 438 HIS cc_start: 0.6263 (m90) cc_final: 0.5245 (m90) REVERT: B 317 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8184 (p) REVERT: D 491 ASP cc_start: 0.8578 (m-30) cc_final: 0.8167 (t0) REVERT: E 341 MET cc_start: 0.8958 (tpp) cc_final: 0.8648 (tpp) REVERT: E 464 ASP cc_start: 0.8722 (m-30) cc_final: 0.8417 (m-30) outliers start: 27 outliers final: 14 residues processed: 118 average time/residue: 0.1179 time to fit residues: 22.9566 Evaluate side-chains 115 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 431 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 22 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 13 optimal weight: 50.0000 chunk 54 optimal weight: 50.0000 chunk 218 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 263 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN ** F 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.101859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.065914 restraints weight = 50948.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.068297 restraints weight = 22325.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.069778 restraints weight = 14232.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.070677 restraints weight = 11155.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.071189 restraints weight = 9694.116| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17389 Z= 0.256 Angle : 0.580 10.743 23723 Z= 0.313 Chirality : 0.045 0.239 2776 Planarity : 0.004 0.096 3058 Dihedral : 10.575 88.696 2595 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.61 % Allowed : 16.38 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.18), residues: 2340 helix: 0.85 (0.19), residues: 848 sheet: -0.92 (0.29), residues: 318 loop : -2.09 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 446 TYR 0.019 0.002 TYR A 388 PHE 0.020 0.002 PHE F 358 TRP 0.035 0.002 TRP A 354 HIS 0.012 0.001 HIS D 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.26 (17389) covalent geometry : angle 0.57988 / 0.31 (23723) hydrogen bonds : bond 0.03755 / 2.86 ( 622) hydrogen bonds : angle 5.08819 / 3.64 ( 1770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 0.739 Fit side-chains REVERT: C 443 GLU cc_start: 0.6514 (pp20) cc_final: 0.6184 (pp20) REVERT: A 354 TRP cc_start: 0.8998 (OUTLIER) cc_final: 0.8747 (t60) REVERT: A 431 CYS cc_start: 0.6696 (m) cc_final: 0.6244 (p) REVERT: A 438 HIS cc_start: 0.6311 (m90) cc_final: 0.5305 (m90) REVERT: B 250 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8173 (m-80) REVERT: D 491 ASP cc_start: 0.8587 (m-30) cc_final: 0.8299 (t0) REVERT: E 464 ASP cc_start: 0.8706 (m-30) cc_final: 0.8440 (m-30) REVERT: F 400 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8944 (t80) outliers start: 37 outliers final: 23 residues processed: 131 average time/residue: 0.1158 time to fit residues: 25.0631 Evaluate side-chains 125 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 431 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 212 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 6 optimal weight: 40.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 263 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 HIS E 449 GLN E 488 ASN F 325 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.104209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.068586 restraints weight = 50331.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.071176 restraints weight = 21525.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.072788 restraints weight = 13455.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.073809 restraints weight = 10382.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 76)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.074352 restraints weight = 8888.993| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17389 Z= 0.111 Angle : 0.475 11.841 23723 Z= 0.258 Chirality : 0.042 0.217 2776 Planarity : 0.003 0.081 3058 Dihedral : 10.367 88.618 2595 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.05 % Allowed : 17.80 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.18), residues: 2340 helix: 1.13 (0.19), residues: 841 sheet: -0.79 (0.30), residues: 311 loop : -1.97 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.015 0.001 TYR A 388 PHE 0.017 0.001 PHE F 358 TRP 0.034 0.002 TRP A 354 HIS 0.007 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (17389) covalent geometry : angle 0.47505 / 0.26 (23723) hydrogen bonds : bond 0.02914 / 2.22 ( 622) hydrogen bonds : angle 4.86371 / 3.48 ( 1770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.600 Fit side-chains REVERT: C 247 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8556 (mt) REVERT: C 443 GLU cc_start: 0.6639 (pp20) cc_final: 0.6249 (pp20) REVERT: A 354 TRP cc_start: 0.9047 (OUTLIER) cc_final: 0.8736 (t60) REVERT: A 429 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7757 (p) REVERT: A 438 HIS cc_start: 0.6375 (m90) cc_final: 0.5351 (m90) REVERT: B 250 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7959 (m-80) REVERT: D 341 MET cc_start: 0.9191 (mmm) cc_final: 0.8971 (tpp) REVERT: D 461 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6828 (mp10) REVERT: D 491 ASP cc_start: 0.8534 (m-30) cc_final: 0.8138 (t0) REVERT: E 341 MET cc_start: 0.8532 (tpt) cc_final: 0.8330 (tpp) REVERT: E 449 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: E 464 ASP cc_start: 0.8645 (m-30) cc_final: 0.8368 (m-30) REVERT: F 397 ASN cc_start: 0.8145 (t0) cc_final: 0.7471 (t0) outliers start: 29 outliers final: 14 residues processed: 130 average time/residue: 0.1160 time to fit residues: 24.8800 Evaluate side-chains 125 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.5980 chunk 194 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 97 optimal weight: 40.0000 chunk 6 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 chunk 222 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 161 optimal weight: 0.6980 chunk 57 optimal weight: 40.0000 chunk 158 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 263 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.104211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.068509 restraints weight = 50829.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.071044 restraints weight = 21450.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.072695 restraints weight = 13448.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.073672 restraints weight = 10309.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.074287 restraints weight = 8889.759| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17389 Z= 0.115 Angle : 0.470 11.859 23723 Z= 0.255 Chirality : 0.041 0.187 2776 Planarity : 0.003 0.077 3058 Dihedral : 10.322 89.290 2595 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.47 % Allowed : 18.15 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.18), residues: 2340 helix: 1.21 (0.19), residues: 838 sheet: -0.76 (0.30), residues: 311 loop : -1.95 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.015 0.001 TYR A 388 PHE 0.017 0.001 PHE F 358 TRP 0.040 0.002 TRP C 354 HIS 0.012 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (17389) covalent geometry : angle 0.46996 / 0.26 (23723) hydrogen bonds : bond 0.02871 / 2.20 ( 622) hydrogen bonds : angle 4.80984 / 3.44 ( 1770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: C 247 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8566 (mt) REVERT: C 443 GLU cc_start: 0.6648 (pp20) cc_final: 0.6252 (pp20) REVERT: A 354 TRP cc_start: 0.9028 (OUTLIER) cc_final: 0.8698 (t60) REVERT: A 429 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7756 (p) REVERT: A 438 HIS cc_start: 0.6380 (m90) cc_final: 0.5342 (m90) REVERT: B 250 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: D 461 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6818 (mp10) REVERT: D 491 ASP cc_start: 0.8555 (m-30) cc_final: 0.8106 (t70) REVERT: E 464 ASP cc_start: 0.8595 (m-30) cc_final: 0.8362 (m-30) REVERT: F 397 ASN cc_start: 0.8129 (t0) cc_final: 0.7453 (t0) outliers start: 35 outliers final: 21 residues processed: 137 average time/residue: 0.1082 time to fit residues: 24.4402 Evaluate side-chains 133 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 22 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 187 optimal weight: 0.3980 chunk 49 optimal weight: 50.0000 chunk 158 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 263 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.104967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.069541 restraints weight = 51273.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.072105 restraints weight = 21600.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.073767 restraints weight = 13498.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.074812 restraints weight = 10352.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.075309 restraints weight = 8843.390| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17389 Z= 0.096 Angle : 0.461 13.058 23723 Z= 0.251 Chirality : 0.041 0.159 2776 Planarity : 0.003 0.070 3058 Dihedral : 10.159 89.688 2595 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.98 % Allowed : 18.86 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.18), residues: 2340 helix: 1.30 (0.19), residues: 838 sheet: -0.69 (0.30), residues: 318 loop : -1.95 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.015 0.001 TYR A 388 PHE 0.019 0.001 PHE F 250 TRP 0.031 0.002 TRP A 354 HIS 0.010 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (17389) covalent geometry : angle 0.46136 / 0.25 (23723) hydrogen bonds : bond 0.02599 / 1.99 ( 622) hydrogen bonds : angle 4.70017 / 3.37 ( 1770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: C 247 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8524 (mt) REVERT: C 443 GLU cc_start: 0.6713 (pp20) cc_final: 0.6308 (pp20) REVERT: A 354 TRP cc_start: 0.9051 (OUTLIER) cc_final: 0.8768 (t60) REVERT: A 429 THR cc_start: 0.7945 (OUTLIER) cc_final: 0.7692 (p) REVERT: A 438 HIS cc_start: 0.6319 (m90) cc_final: 0.5287 (m90) REVERT: B 250 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: D 248 VAL cc_start: 0.8752 (t) cc_final: 0.8459 (p) REVERT: D 341 MET cc_start: 0.9224 (mmm) cc_final: 0.8999 (tpp) REVERT: D 461 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6668 (mp10) REVERT: D 491 ASP cc_start: 0.8488 (m-30) cc_final: 0.8071 (t70) REVERT: E 358 PHE cc_start: 0.8798 (t80) cc_final: 0.8092 (t80) REVERT: E 464 ASP cc_start: 0.8567 (m-30) cc_final: 0.8325 (m-30) REVERT: F 397 ASN cc_start: 0.7993 (t0) cc_final: 0.7387 (t0) outliers start: 28 outliers final: 17 residues processed: 133 average time/residue: 0.1097 time to fit residues: 24.0990 Evaluate side-chains 130 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 56 optimal weight: 50.0000 chunk 149 optimal weight: 40.0000 chunk 142 optimal weight: 40.0000 chunk 85 optimal weight: 0.9990 chunk 51 optimal weight: 40.0000 chunk 105 optimal weight: 0.0870 chunk 12 optimal weight: 30.0000 chunk 133 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 217 optimal weight: 0.4980 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN E 449 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.104423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.068842 restraints weight = 51282.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071391 restraints weight = 21541.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.073054 restraints weight = 13491.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 72)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.074072 restraints weight = 10317.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.074579 restraints weight = 8820.477| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17389 Z= 0.113 Angle : 0.472 14.007 23723 Z= 0.255 Chirality : 0.041 0.277 2776 Planarity : 0.003 0.073 3058 Dihedral : 10.174 89.135 2595 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 2.19 % Allowed : 19.21 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.18), residues: 2340 helix: 1.31 (0.19), residues: 837 sheet: -0.68 (0.30), residues: 318 loop : -1.93 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 446 TYR 0.014 0.001 TYR A 388 PHE 0.015 0.001 PHE F 358 TRP 0.030 0.002 TRP A 354 HIS 0.010 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (17389) covalent geometry : angle 0.47173 / 0.25 (23723) hydrogen bonds : bond 0.02697 / 2.07 ( 622) hydrogen bonds : angle 4.68084 / 3.35 ( 1770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: C 247 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8532 (mt) REVERT: C 443 GLU cc_start: 0.6700 (pp20) cc_final: 0.6308 (pp20) REVERT: A 354 TRP cc_start: 0.9056 (OUTLIER) cc_final: 0.8752 (t60) REVERT: A 429 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7706 (p) REVERT: A 438 HIS cc_start: 0.6331 (m90) cc_final: 0.5301 (m90) REVERT: B 250 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: D 248 VAL cc_start: 0.8783 (t) cc_final: 0.8489 (p) REVERT: D 461 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6627 (mp10) REVERT: D 491 ASP cc_start: 0.8458 (m-30) cc_final: 0.8156 (t70) REVERT: E 449 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7779 (pm20) REVERT: E 464 ASP cc_start: 0.8577 (m-30) cc_final: 0.8319 (m-30) REVERT: F 397 ASN cc_start: 0.7969 (t0) cc_final: 0.7272 (t0) outliers start: 31 outliers final: 22 residues processed: 129 average time/residue: 0.1088 time to fit residues: 22.9924 Evaluate side-chains 133 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Chi-restraints excluded: chain F residue 466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 50 optimal weight: 50.0000 chunk 100 optimal weight: 50.0000 chunk 127 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 48 optimal weight: 50.0000 chunk 145 optimal weight: 50.0000 chunk 218 optimal weight: 0.7980 chunk 97 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN ** F 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.105867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.070123 restraints weight = 50874.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.072766 restraints weight = 21949.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.074329 restraints weight = 13781.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.075296 restraints weight = 10792.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.075706 restraints weight = 9334.280| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17389 Z= 0.212 Angle : 0.550 14.131 23723 Z= 0.294 Chirality : 0.044 0.278 2776 Planarity : 0.003 0.072 3058 Dihedral : 10.336 88.377 2595 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 2.12 % Allowed : 19.28 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.18), residues: 2340 helix: 1.16 (0.19), residues: 843 sheet: -0.89 (0.29), residues: 323 loop : -1.91 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 423 TYR 0.013 0.001 TYR A 388 PHE 0.020 0.002 PHE B 293 TRP 0.031 0.002 TRP C 354 HIS 0.012 0.001 HIS D 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (17389) covalent geometry : angle 0.54983 / 0.29 (23723) hydrogen bonds : bond 0.03279 / 2.51 ( 622) hydrogen bonds : angle 4.84090 / 3.47 ( 1770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 247 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8703 (mt) REVERT: C 443 GLU cc_start: 0.6774 (pp20) cc_final: 0.6377 (pp20) REVERT: A 354 TRP cc_start: 0.9043 (OUTLIER) cc_final: 0.8747 (t60) REVERT: A 429 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7867 (p) REVERT: A 438 HIS cc_start: 0.6431 (m90) cc_final: 0.5415 (m90) REVERT: B 250 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8111 (m-80) REVERT: D 461 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.7110 (mp10) REVERT: E 464 ASP cc_start: 0.8558 (m-30) cc_final: 0.8343 (m-30) REVERT: F 397 ASN cc_start: 0.8060 (t0) cc_final: 0.7389 (t0) outliers start: 30 outliers final: 21 residues processed: 122 average time/residue: 0.1115 time to fit residues: 22.5553 Evaluate side-chains 123 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 137 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 54 optimal weight: 50.0000 chunk 218 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 40.0000 chunk 32 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN E 488 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.104020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068270 restraints weight = 51297.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.070873 restraints weight = 21872.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072502 restraints weight = 13650.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.073484 restraints weight = 10519.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.074061 restraints weight = 9027.972| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17389 Z= 0.119 Angle : 0.479 14.496 23723 Z= 0.258 Chirality : 0.042 0.268 2776 Planarity : 0.003 0.065 3058 Dihedral : 10.199 88.788 2595 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.05 % Allowed : 19.21 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.18), residues: 2340 helix: 1.28 (0.19), residues: 838 sheet: -0.84 (0.30), residues: 321 loop : -1.93 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.014 0.001 TYR A 388 PHE 0.015 0.001 PHE F 358 TRP 0.030 0.002 TRP A 354 HIS 0.009 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (17389) covalent geometry : angle 0.47878 / 0.26 (23723) hydrogen bonds : bond 0.02749 / 2.10 ( 622) hydrogen bonds : angle 4.71730 / 3.38 ( 1770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3775.26 seconds wall clock time: 65 minutes 29.49 seconds (3929.49 seconds total)