Starting phenix.real_space_refine on Sat Jul 4 01:12:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e2l_27842/07_2026/8e2l_27842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2l_27842/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8e2l_27842/07_2026/8e2l_27842.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e2l_27842/07_2026/8e2l_27842.cif" model { file = "/net/cci-nas-00/data/ceres_data/8e2l_27842/07_2026/8e2l_27842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2l_27842/07_2026/8e2l_27842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e2l_27842/07_2026/8e2l_27842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2l_27842/07_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-dev-6108/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: 4.00, per 1000 atoms: 0.23 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: 1.38 Conformation dependent library (CDL) restraints added in 697.2 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: 0.50 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: 2.45 Time building geometry restraints manager: 1.82 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.710 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- 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 0.73680 / 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 : 0.621 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: 0.1163 time to fit residues: 27.6165 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 : 0.664 ------------------------------------------------------------------------------- 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 C 432 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.105909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070430 restraints weight = 50526.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.073087 restraints weight = 21580.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.074805 restraints weight = 13428.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.075680 restraints weight = 10285.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076372 restraints weight = 8935.407| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17389 Z= 0.172 Angle : 0.536 13.796 23723 Z= 0.293 Chirality : 0.043 0.270 2776 Planarity : 0.004 0.090 3058 Dihedral : 10.594 89.958 2595 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.82 % Favored : 92.14 % Rotamer: Outliers : 1.06 % Allowed : 7.77 % Favored : 91.17 % 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: -0.99 (0.18), residues: 2340 helix: 0.84 (0.19), residues: 837 sheet: -0.07 (0.31), residues: 327 loop : -2.04 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.022 0.002 TYR A 351 PHE 0.032 0.002 PHE F 358 TRP 0.022 0.002 TRP C 195 HIS 0.010 0.001 HIS D 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (17389) covalent geometry : angle 0.53642 / 0.29 (23723) hydrogen bonds : bond 0.04137 / 3.15 ( 622) hydrogen bonds : angle 5.44668 / 3.90 ( 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 134 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 402 MET cc_start: 0.8366 (tmm) cc_final: 0.8040 (tmm) REVERT: A 386 TYR cc_start: 0.8639 (m-80) cc_final: 0.8149 (m-80) REVERT: A 402 MET cc_start: 0.7301 (tmm) cc_final: 0.7081 (tmm) REVERT: A 438 HIS cc_start: 0.6360 (m90) cc_final: 0.5494 (m90) REVERT: B 491 ASP cc_start: 0.8355 (m-30) cc_final: 0.8099 (m-30) REVERT: E 464 ASP cc_start: 0.8706 (m-30) cc_final: 0.8375 (m-30) outliers start: 15 outliers final: 10 residues processed: 123 average time/residue: 0.1176 time to fit residues: 23.2867 Evaluate side-chains 115 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 354 TRP 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 Chi-restraints excluded: chain F residue 400 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: 6.9990 chunk 142 optimal weight: 40.0000 chunk 89 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 40.0000 chunk 24 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 224 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 484 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.105565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070031 restraints weight = 50853.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.072699 restraints weight = 21403.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.074383 restraints weight = 13261.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.075411 restraints weight = 10158.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.075968 restraints weight = 8680.770| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17389 Z= 0.141 Angle : 0.485 13.083 23723 Z= 0.266 Chirality : 0.042 0.205 2776 Planarity : 0.003 0.097 3058 Dihedral : 10.505 89.308 2595 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.13 % Allowed : 11.72 % Favored : 87.15 % 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: 0.97 (0.19), residues: 838 sheet: -0.16 (0.31), residues: 325 loop : -2.02 (0.18), residues: 1177 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 0.028 0.001 PHE F 358 TRP 0.030 0.002 TRP C 354 HIS 0.008 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (17389) covalent geometry : angle 0.48500 / 0.27 (23723) hydrogen bonds : bond 0.03604 / 2.74 ( 622) hydrogen bonds : angle 5.09309 / 3.65 ( 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: 16 poor density : 116 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.7455 (tmm) cc_final: 0.7235 (tmm) REVERT: A 438 HIS cc_start: 0.6315 (m90) cc_final: 0.5406 (m90) REVERT: B 491 ASP cc_start: 0.8450 (m-30) cc_final: 0.8249 (m-30) REVERT: E 402 MET cc_start: 0.7426 (tmm) cc_final: 0.7062 (tmm) REVERT: E 464 ASP cc_start: 0.8691 (m-30) cc_final: 0.8398 (m-30) REVERT: F 397 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.6911 (t0) REVERT: F 400 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.9002 (m-80) outliers start: 16 outliers final: 10 residues processed: 122 average time/residue: 0.1207 time to fit residues: 23.9591 Evaluate side-chains 119 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain B residue 317 VAL 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 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: 50.0000 chunk 97 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 163 optimal weight: 2.9990 chunk 180 optimal weight: 0.3980 chunk 161 optimal weight: 0.9990 chunk 140 optimal weight: 30.0000 chunk 235 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 142 optimal weight: 40.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 ** E 449 GLN ** 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 = 0.3994 r_free = 0.3994 target = 0.103240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.067429 restraints weight = 51147.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.069990 restraints weight = 22126.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.071579 restraints weight = 13852.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.072517 restraints weight = 10715.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.073074 restraints weight = 9273.538| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2007 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= 0.207 Angle : 0.542 11.443 23723 Z= 0.294 Chirality : 0.044 0.261 2776 Planarity : 0.004 0.091 3058 Dihedral : 10.616 89.800 2595 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.12 % Allowed : 13.77 % Favored : 84.11 % 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: -1.08 (0.18), residues: 2340 helix: 0.86 (0.19), residues: 847 sheet: -0.55 (0.30), residues: 325 loop : -2.04 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 343 TYR 0.015 0.002 TYR A 388 PHE 0.021 0.002 PHE F 358 TRP 0.043 0.002 TRP A 354 HIS 0.009 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (17389) covalent geometry : angle 0.54212 / 0.29 (23723) hydrogen bonds : bond 0.03683 / 2.81 ( 622) hydrogen bonds : angle 5.02783 / 3.60 ( 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 138 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: C 402 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7977 (tmm) REVERT: A 438 HIS cc_start: 0.6230 (m90) cc_final: 0.5245 (m90) REVERT: B 317 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8209 (p) REVERT: D 491 ASP cc_start: 0.8562 (m-30) cc_final: 0.8168 (t0) REVERT: E 402 MET cc_start: 0.7674 (tmm) cc_final: 0.7438 (tmm) REVERT: E 464 ASP cc_start: 0.8733 (m-30) cc_final: 0.8436 (m-30) REVERT: F 397 ASN cc_start: 0.8087 (t0) cc_final: 0.7482 (t0) outliers start: 30 outliers final: 20 residues processed: 123 average time/residue: 0.1168 time to fit residues: 23.5482 Evaluate side-chains 123 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 335 MET 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: 0.0980 chunk 145 optimal weight: 0.7980 chunk 151 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 13 optimal weight: 50.0000 chunk 54 optimal weight: 50.0000 chunk 218 optimal weight: 6.9990 chunk 231 optimal weight: 0.3980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 GLN ** 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 = 0.4017 r_free = 0.4017 target = 0.104529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.068876 restraints weight = 50557.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071487 restraints weight = 21561.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073091 restraints weight = 13438.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.074081 restraints weight = 10385.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.074596 restraints weight = 8902.657| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17389 Z= 0.127 Angle : 0.475 12.348 23723 Z= 0.259 Chirality : 0.041 0.179 2776 Planarity : 0.003 0.092 3058 Dihedral : 10.452 89.179 2595 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.84 % Allowed : 15.96 % Favored : 82.20 % 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: -0.91 (0.18), residues: 2340 helix: 1.07 (0.19), residues: 842 sheet: -0.51 (0.30), residues: 322 loop : -1.96 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 254 TYR 0.015 0.001 TYR A 388 PHE 0.019 0.001 PHE F 358 TRP 0.033 0.001 TRP A 354 HIS 0.007 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (17389) covalent geometry : angle 0.47506 / 0.26 (23723) hydrogen bonds : bond 0.03105 / 2.37 ( 622) hydrogen bonds : angle 4.85047 / 3.47 ( 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 139 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 HIS cc_start: 0.6148 (m90) cc_final: 0.5181 (m90) REVERT: B 317 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8235 (p) REVERT: D 491 ASP cc_start: 0.8527 (m-30) cc_final: 0.8143 (t0) REVERT: E 464 ASP cc_start: 0.8717 (m-30) cc_final: 0.8434 (m-30) REVERT: F 397 ASN cc_start: 0.8007 (t0) cc_final: 0.7429 (t0) outliers start: 26 outliers final: 15 residues processed: 127 average time/residue: 0.1118 time to fit residues: 23.1414 Evaluate side-chains 124 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 401 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B 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 335 MET Chi-restraints excluded: chain E residue 427 THR 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: 0.0040 chunk 121 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 18 optimal weight: 30.0000 chunk 212 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 6 optimal weight: 50.0000 overall best weight: 2.8000 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN ** 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 = 0.3981 r_free = 0.3981 target = 0.102462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.066408 restraints weight = 50726.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.068838 restraints weight = 22055.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.070387 restraints weight = 14006.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.071332 restraints weight = 10863.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.071797 restraints weight = 9364.385| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 0.005 0.049 17389 Z= 0.233 Angle : 0.563 10.618 23723 Z= 0.304 Chirality : 0.044 0.194 2776 Planarity : 0.004 0.085 3058 Dihedral : 10.545 88.763 2595 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 2.33 % Allowed : 16.81 % Favored : 80.86 % 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: -1.10 (0.18), residues: 2340 helix: 0.94 (0.19), residues: 843 sheet: -0.85 (0.29), residues: 318 loop : -2.01 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 423 TYR 0.020 0.002 TYR A 388 PHE 0.021 0.002 PHE B 293 TRP 0.039 0.002 TRP A 354 HIS 0.011 0.001 HIS D 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (17389) covalent geometry : angle 0.56301 / 0.30 (23723) hydrogen bonds : bond 0.03664 / 2.79 ( 622) hydrogen bonds : angle 5.01803 / 3.61 ( 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 142 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 402 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.8024 (tmm) REVERT: C 443 GLU cc_start: 0.6597 (pp20) cc_final: 0.6086 (pp20) REVERT: A 438 HIS cc_start: 0.6334 (m90) cc_final: 0.5337 (m90) REVERT: B 250 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: D 491 ASP cc_start: 0.8596 (m-30) cc_final: 0.8284 (t0) REVERT: E 464 ASP cc_start: 0.8676 (m-30) cc_final: 0.8403 (m-30) REVERT: F 397 ASN cc_start: 0.8087 (t0) cc_final: 0.7546 (t0) REVERT: F 402 MET cc_start: 0.8081 (mmm) cc_final: 0.7869 (mmm) outliers start: 33 outliers final: 20 residues processed: 130 average time/residue: 0.0939 time to fit residues: 20.2227 Evaluate side-chains 122 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 466 VAL Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 427 THR 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 335 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 97 optimal weight: 30.0000 chunk 6 optimal weight: 50.0000 chunk 96 optimal weight: 30.0000 chunk 222 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 161 optimal weight: 0.3980 chunk 57 optimal weight: 40.0000 chunk 158 optimal weight: 9.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 GLN ** E 449 GLN ** 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 = 0.3987 r_free = 0.3987 target = 0.102801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.066958 restraints weight = 50594.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.069435 restraints weight = 21939.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070989 restraints weight = 13844.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.071955 restraints weight = 10753.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.072439 restraints weight = 9292.040| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17389 Z= 0.188 Angle : 0.524 11.233 23723 Z= 0.284 Chirality : 0.043 0.149 2776 Planarity : 0.003 0.086 3058 Dihedral : 10.455 89.733 2595 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 2.54 % Allowed : 17.09 % Favored : 80.37 % 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: -1.07 (0.18), residues: 2340 helix: 0.99 (0.19), residues: 843 sheet: -0.95 (0.29), residues: 318 loop : -1.99 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 286 TYR 0.015 0.001 TYR A 388 PHE 0.029 0.002 PHE B 358 TRP 0.048 0.002 TRP C 354 HIS 0.011 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (17389) covalent geometry : angle 0.52411 / 0.28 (23723) hydrogen bonds : bond 0.03268 / 2.49 ( 622) hydrogen bonds : angle 4.93173 / 3.54 ( 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 143 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 443 GLU cc_start: 0.6633 (pp20) cc_final: 0.6253 (pp20) REVERT: A 429 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7587 (p) REVERT: A 431 CYS cc_start: 0.6663 (m) cc_final: 0.6351 (p) REVERT: A 438 HIS cc_start: 0.6402 (m90) cc_final: 0.5379 (m90) REVERT: B 250 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.8050 (m-80) REVERT: D 461 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6814 (mp10) REVERT: D 491 ASP cc_start: 0.8563 (m-30) cc_final: 0.8284 (t0) REVERT: E 464 ASP cc_start: 0.8676 (m-30) cc_final: 0.8414 (m-30) REVERT: F 397 ASN cc_start: 0.8033 (t0) cc_final: 0.7501 (t0) outliers start: 36 outliers final: 20 residues processed: 129 average time/residue: 0.1068 time to fit residues: 22.6304 Evaluate side-chains 128 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 319 THR 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 335 MET 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 466 VAL 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: 0.9990 chunk 215 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 49 optimal weight: 50.0000 chunk 158 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN E 449 GLN E 488 ASN F 342 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.103371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.067641 restraints weight = 50959.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.070184 restraints weight = 21815.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.071755 restraints weight = 13660.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 74)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.072716 restraints weight = 10579.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073210 restraints weight = 9104.555| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17389 Z= 0.142 Angle : 0.500 12.571 23723 Z= 0.270 Chirality : 0.042 0.154 2776 Planarity : 0.003 0.082 3058 Dihedral : 10.389 89.887 2595 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 2.19 % Allowed : 17.44 % Favored : 80.37 % 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: -1.00 (0.18), residues: 2340 helix: 1.06 (0.19), residues: 843 sheet: -0.93 (0.29), residues: 318 loop : -1.94 (0.18), residues: 1179 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 0.020 0.001 PHE B 358 TRP 0.032 0.002 TRP C 354 HIS 0.011 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (17389) covalent geometry : angle 0.50012 / 0.27 (23723) hydrogen bonds : bond 0.03104 / 2.36 ( 622) hydrogen bonds : angle 4.87257 / 3.50 ( 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 140 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 247 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8612 (mt) REVERT: C 443 GLU cc_start: 0.6633 (pp20) cc_final: 0.6249 (pp20) REVERT: A 429 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7553 (p) REVERT: A 431 CYS cc_start: 0.6524 (m) cc_final: 0.6268 (p) REVERT: A 438 HIS cc_start: 0.6354 (m90) cc_final: 0.5349 (m90) REVERT: B 250 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: D 491 ASP cc_start: 0.8559 (m-30) cc_final: 0.8267 (t0) REVERT: E 464 ASP cc_start: 0.8605 (m-30) cc_final: 0.8354 (m-30) REVERT: E 491 ASP cc_start: 0.8086 (m-30) cc_final: 0.7735 (t0) REVERT: F 366 MET cc_start: 0.7747 (mtm) cc_final: 0.7492 (mtm) REVERT: F 397 ASN cc_start: 0.8030 (t0) cc_final: 0.7523 (t0) outliers start: 31 outliers final: 21 residues processed: 130 average time/residue: 0.1028 time to fit residues: 22.1392 Evaluate side-chains 130 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 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 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 319 THR Chi-restraints excluded: chain E residue 335 MET 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 443 GLU 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: 9.9990 chunk 51 optimal weight: 40.0000 chunk 105 optimal weight: 40.0000 chunk 12 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 263 ASN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN ** F 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.101984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.065926 restraints weight = 52357.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.068183 restraints weight = 24557.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.069631 restraints weight = 16144.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.070466 restraints weight = 12726.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.070935 restraints weight = 11216.168| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.099 17389 Z= 0.477 Angle : 0.835 11.343 23723 Z= 0.441 Chirality : 0.051 0.213 2776 Planarity : 0.005 0.085 3058 Dihedral : 10.818 88.878 2595 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.31 % Favored : 87.56 % Rotamer: Outliers : 2.82 % Allowed : 18.08 % Favored : 79.10 % 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: -1.91 (0.17), residues: 2340 helix: 0.20 (0.19), residues: 848 sheet: -1.62 (0.28), residues: 343 loop : -2.35 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 423 TYR 0.024 0.003 TYR C 258 PHE 0.037 0.003 PHE B 293 TRP 0.042 0.003 TRP C 354 HIS 0.018 0.002 HIS D 438 Details of bonding type rmsd/Z covalent geometry : bond 0.01103 / 0.48 (17389) covalent geometry : angle 0.83509 / 0.44 (23723) hydrogen bonds : bond 0.04982 / 3.79 ( 622) hydrogen bonds : angle 5.61329 / 4.03 ( 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 143 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 103 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 443 GLU cc_start: 0.6849 (pp20) cc_final: 0.6538 (pp20) REVERT: A 429 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7915 (p) REVERT: E 251 LYS cc_start: 0.8641 (pttp) cc_final: 0.8337 (tppt) REVERT: E 464 ASP cc_start: 0.8520 (m-30) cc_final: 0.7613 (t0) outliers start: 40 outliers final: 25 residues processed: 132 average time/residue: 0.1115 time to fit residues: 24.1741 Evaluate side-chains 121 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 263 ASN 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 506 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 348 LEU 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 335 MET Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 335 MET 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: 30.0000 chunk 127 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 50.0000 chunk 145 optimal weight: 0.0970 chunk 218 optimal weight: 0.9990 chunk 97 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 68 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 GLN ** 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 = 0.4012 r_free = 0.4012 target = 0.102600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.067600 restraints weight = 51869.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070303 restraints weight = 26697.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.070851 restraints weight = 15854.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071025 restraints weight = 13009.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.071242 restraints weight = 12167.334| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.120 17389 Z= 0.352 Angle : 0.947 59.200 23723 Z= 0.522 Chirality : 0.050 0.546 2776 Planarity : 0.005 0.085 3058 Dihedral : 10.834 89.192 2595 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.14 % Favored : 87.65 % Rotamer: Outliers : 2.19 % Allowed : 19.21 % Favored : 78.60 % 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: -1.94 (0.17), residues: 2340 helix: 0.17 (0.19), residues: 848 sheet: -1.65 (0.27), residues: 345 loop : -2.34 (0.17), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 286 TYR 0.018 0.002 TYR C 258 PHE 0.029 0.003 PHE B 293 TRP 0.037 0.003 TRP C 354 HIS 0.015 0.002 HIS D 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00809 / 0.35 (17389) covalent geometry : angle 0.94651 / 0.52 (23723) hydrogen bonds : bond 0.04794 / 3.66 ( 622) hydrogen bonds : angle 5.58014 / 4.00 ( 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 125 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 443 GLU cc_start: 0.6831 (pp20) cc_final: 0.6569 (pp20) REVERT: A 429 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.8074 (p) REVERT: E 251 LYS cc_start: 0.8627 (pttp) cc_final: 0.8298 (tppt) REVERT: E 464 ASP cc_start: 0.8487 (m-30) cc_final: 0.7609 (t0) outliers start: 31 outliers final: 27 residues processed: 116 average time/residue: 0.1239 time to fit residues: 23.4541 Evaluate side-chains 121 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 429 THR 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 348 LEU 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 318 ASN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 335 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 137 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 194 optimal weight: 0.7980 chunk 54 optimal weight: 50.0000 chunk 218 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 51 optimal weight: 40.0000 chunk 32 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.102606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.067618 restraints weight = 52211.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.070230 restraints weight = 26781.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.070702 restraints weight = 15848.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.070924 restraints weight = 13209.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.071196 restraints weight = 12442.791| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.120 17389 Z= 0.352 Angle : 0.947 59.200 23723 Z= 0.522 Chirality : 0.050 0.546 2776 Planarity : 0.005 0.085 3058 Dihedral : 10.834 89.192 2595 Min Nonbonded Distance : 1.405 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.14 % Favored : 87.65 % Rotamer: Outliers : 1.98 % Allowed : 19.49 % Favored : 78.53 % 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: -1.94 (0.17), residues: 2340 helix: 0.17 (0.19), residues: 848 sheet: -1.65 (0.27), residues: 345 loop : -2.34 (0.17), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 286 TYR 0.018 0.002 TYR C 258 PHE 0.029 0.003 PHE B 293 TRP 0.037 0.003 TRP C 354 HIS 0.015 0.002 HIS D 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00809 / 0.35 (17389) covalent geometry : angle 0.94651 / 0.52 (23723) hydrogen bonds : bond 0.04794 / 3.66 ( 622) hydrogen bonds : angle 5.58014 / 4.00 ( 1770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3407.75 seconds wall clock time: 59 minutes 20.27 seconds (3560.27 seconds total)