Starting phenix.real_space_refine on Sun Aug 24 05:41:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e2l_27842/08_2025/8e2l_27842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2l_27842/08_2025/8e2l_27842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e2l_27842/08_2025/8e2l_27842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2l_27842/08_2025/8e2l_27842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e2l_27842/08_2025/8e2l_27842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2l_27842/08_2025/8e2l_27842.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 27 5.49 5 Mg 5 5.21 5 S 54 5.16 5 C 10698 2.51 5 N 3027 2.21 5 O 3281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17092 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3122 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 7, 'GLN:plan1': 5, 'PHE:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 12, 'TRP:plan': 2, 'TYR:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 260 Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3114 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 7, 'GLN:plan1': 5, 'PHE:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 12, 'TRP:plan': 2, 'TYR:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 260 Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3122 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 7, 'GLN:plan1': 5, 'PHE:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 12, 'TRP:plan': 2, 'TYR:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 260 Chain: "D" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3122 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 7, 'GLN:plan1': 5, 'PHE:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 12, 'TRP:plan': 2, 'TYR:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 260 Chain: "E" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2145 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2067 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain breaks: 2 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.90, 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: 1.11 Conformation dependent library (CDL) restraints added in 546.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.42 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: 2.26 Time building geometry restraints manager: 1.47 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: 9677 23.41 - 46.81: 536 46.81 - 70.22: 109 70.22 - 93.62: 25 93.62 - 117.03: 1 Dihedral angle restraints: 10348 sinusoidal: 3515 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 10345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2512 0.077 - 0.153: 252 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: 2.190 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.830 Find NCS groups from input model: 0.310 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 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= 0.291 Angle : 0.729 20.135 23723 Z= 0.559 Chirality : 0.045 0.383 2776 Planarity : 0.003 0.055 3058 Dihedral : 15.288 117.029 5904 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 aren 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 covalent geometry : bond 0.00365 (17389) covalent geometry : angle 0.72875 (23723) hydrogen bonds : bond 0.21066 ( 622) hydrogen bonds : angle 7.60123 ( 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 : 0.570 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: 0.1364 time to fit residues: 31.6869 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 : 0.653 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 397 ASN ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS D 369 HIS E 432 HIS ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.105821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.070316 restraints weight = 50540.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072988 restraints weight = 21620.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074682 restraints weight = 13426.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.075730 restraints weight = 10291.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076267 restraints weight = 8777.412| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17389 Z= 0.174 Angle : 0.529 12.327 23723 Z= 0.291 Chirality : 0.043 0.243 2776 Planarity : 0.004 0.083 3058 Dihedral : 10.623 88.539 2750 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 1.06 % Allowed : 7.34 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.18), residues: 2340 helix: 0.94 (0.19), residues: 831 sheet: -0.04 (0.31), residues: 327 loop : -2.02 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 286 TYR 0.021 0.001 TYR C 386 PHE 0.026 0.002 PHE B 358 TRP 0.018 0.002 TRP A 354 HIS 0.011 0.001 HIS D 369 Details of bonding type rmsd covalent geometry : bond 0.00390 (17389) covalent geometry : angle 0.52910 (23723) hydrogen bonds : bond 0.04595 ( 622) hydrogen bonds : angle 5.49186 ( 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 137 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8646 (m-80) cc_final: 0.8181 (m-80) REVERT: A 402 MET cc_start: 0.7401 (tmm) cc_final: 0.7193 (tmm) REVERT: A 438 HIS cc_start: 0.6295 (m90) cc_final: 0.5463 (m90) REVERT: B 491 ASP cc_start: 0.8380 (m-30) cc_final: 0.8128 (m-30) REVERT: E 464 ASP cc_start: 0.8704 (m-30) cc_final: 0.8369 (m-30) outliers start: 15 outliers final: 10 residues processed: 126 average time/residue: 0.1088 time to fit residues: 22.1485 Evaluate side-chains 118 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 317 VAL 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: 0.1980 chunk 87 optimal weight: 5.9990 chunk 142 optimal weight: 40.0000 chunk 89 optimal weight: 0.1980 chunk 137 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 50.0000 chunk 24 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 224 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 484 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.106040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.070537 restraints weight = 50768.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.073234 restraints weight = 21672.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.074933 restraints weight = 13453.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.075973 restraints weight = 10292.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.076534 restraints weight = 8786.533| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1582 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= 0.127 Angle : 0.473 11.085 23723 Z= 0.260 Chirality : 0.041 0.209 2776 Planarity : 0.003 0.093 3058 Dihedral : 10.646 89.269 2750 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.34 % Allowed : 11.86 % Favored : 86.79 % 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 aren not related in a simple way. whole: -0.87 (0.18), residues: 2340 helix: 1.00 (0.19), residues: 838 sheet: -0.15 (0.31), residues: 319 loop : -1.96 (0.18), residues: 1183 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 0.027 0.001 PHE F 358 TRP 0.032 0.002 TRP A 354 HIS 0.009 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00283 (17389) covalent geometry : angle 0.47311 (23723) hydrogen bonds : bond 0.03361 ( 622) hydrogen bonds : angle 5.00769 ( 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 138 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.7425 (tmm) cc_final: 0.7181 (tmm) REVERT: A 438 HIS cc_start: 0.6319 (m90) cc_final: 0.5422 (m90) REVERT: D 341 MET cc_start: 0.8921 (tpp) cc_final: 0.8682 (tpt) REVERT: E 341 MET cc_start: 0.8999 (tpp) cc_final: 0.8734 (tpp) REVERT: E 464 ASP cc_start: 0.8749 (m-30) cc_final: 0.8456 (m-30) REVERT: F 397 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.6881 (t0) outliers start: 19 outliers final: 12 residues processed: 124 average time/residue: 0.1121 time to fit residues: 22.5823 Evaluate side-chains 125 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 445 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 401 MET 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 F residue 250 PHE Chi-restraints excluded: chain F residue 397 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 47 optimal weight: 40.0000 chunk 97 optimal weight: 30.0000 chunk 87 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 140 optimal weight: 40.0000 chunk 235 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 142 optimal weight: 40.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 ASN C 432 HIS ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** 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 = 0.4008 r_free = 0.4008 target = 0.104048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.068303 restraints weight = 50848.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070911 restraints weight = 21587.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072580 restraints weight = 13407.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.073580 restraints weight = 10289.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.074146 restraints weight = 8822.181| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17389 Z= 0.173 Angle : 0.504 9.756 23723 Z= 0.276 Chirality : 0.043 0.253 2776 Planarity : 0.003 0.086 3058 Dihedral : 10.884 87.807 2750 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.76 % Favored : 91.20 % Rotamer: Outliers : 2.05 % Allowed : 12.92 % Favored : 85.03 % 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 aren not related in a simple way. whole: -0.93 (0.18), residues: 2340 helix: 1.04 (0.19), residues: 839 sheet: -0.41 (0.30), residues: 319 loop : -1.98 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 481 TYR 0.015 0.001 TYR A 388 PHE 0.023 0.002 PHE B 490 TRP 0.027 0.002 TRP A 354 HIS 0.010 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00394 (17389) covalent geometry : angle 0.50388 (23723) hydrogen bonds : bond 0.03382 ( 622) hydrogen bonds : angle 4.87774 ( 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 144 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: C 402 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.8003 (tmm) REVERT: A 438 HIS cc_start: 0.6201 (m90) cc_final: 0.5230 (m90) REVERT: B 317 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8211 (p) REVERT: D 491 ASP cc_start: 0.8577 (m-30) cc_final: 0.8148 (t0) REVERT: E 464 ASP cc_start: 0.8718 (m-30) cc_final: 0.8435 (m-30) REVERT: F 402 MET cc_start: 0.8160 (mtp) cc_final: 0.7880 (tpt) outliers start: 29 outliers final: 16 residues processed: 128 average time/residue: 0.0966 time to fit residues: 20.3551 Evaluate side-chains 124 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 381 MET 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 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: 0.8980 chunk 145 optimal weight: 50.0000 chunk 151 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 13 optimal weight: 50.0000 chunk 54 optimal weight: 50.0000 chunk 218 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN ** F 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.102831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066927 restraints weight = 50863.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.069476 restraints weight = 21775.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.071036 restraints weight = 13623.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.072000 restraints weight = 10567.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072504 restraints weight = 9098.470| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17389 Z= 0.217 Angle : 0.546 9.126 23723 Z= 0.298 Chirality : 0.044 0.190 2776 Planarity : 0.003 0.086 3058 Dihedral : 11.144 86.238 2750 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 2.19 % Allowed : 15.54 % Favored : 82.27 % 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 aren not related in a simple way. whole: -1.04 (0.18), residues: 2340 helix: 0.97 (0.19), residues: 841 sheet: -0.78 (0.30), residues: 318 loop : -1.98 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 481 TYR 0.016 0.002 TYR A 388 PHE 0.021 0.002 PHE E 250 TRP 0.028 0.002 TRP A 354 HIS 0.008 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00501 (17389) covalent geometry : angle 0.54602 (23723) hydrogen bonds : bond 0.03511 ( 622) hydrogen bonds : angle 4.92015 ( 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 140 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: C 402 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7997 (tmm) REVERT: C 443 GLU cc_start: 0.6587 (pp20) cc_final: 0.6078 (pp20) REVERT: A 438 HIS cc_start: 0.6332 (m90) cc_final: 0.5371 (m90) REVERT: B 250 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: D 491 ASP cc_start: 0.8583 (m-30) cc_final: 0.8271 (t0) REVERT: E 341 MET cc_start: 0.8648 (tpt) cc_final: 0.8436 (tpp) REVERT: E 464 ASP cc_start: 0.8707 (m-30) cc_final: 0.8410 (m-30) REVERT: F 397 ASN cc_start: 0.8142 (t0) cc_final: 0.7429 (t0) outliers start: 31 outliers final: 17 residues processed: 127 average time/residue: 0.0950 time to fit residues: 19.8423 Evaluate side-chains 120 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 B residue 250 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 431 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 378 LEU 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: 20.0000 chunk 121 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 18 optimal weight: 40.0000 chunk 212 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 6 optimal weight: 50.0000 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 HIS E 325 GLN ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN ** F 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.103826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068094 restraints weight = 50620.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.070647 restraints weight = 21461.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072315 restraints weight = 13490.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.073305 restraints weight = 10313.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.073889 restraints weight = 8848.843| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2504 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 : 0.486 10.627 23723 Z= 0.265 Chirality : 0.042 0.158 2776 Planarity : 0.003 0.075 3058 Dihedral : 11.076 88.284 2750 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 2.05 % Allowed : 16.88 % Favored : 81.07 % 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 aren not related in a simple way. whole: -0.94 (0.18), residues: 2340 helix: 1.13 (0.19), residues: 838 sheet: -0.79 (0.30), residues: 311 loop : -1.95 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.015 0.001 TYR A 388 PHE 0.020 0.001 PHE F 358 TRP 0.041 0.002 TRP C 354 HIS 0.008 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00324 (17389) covalent geometry : angle 0.48586 (23723) hydrogen bonds : bond 0.02967 ( 622) hydrogen bonds : angle 4.79770 ( 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: 29 poor density : 113 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: C 443 GLU cc_start: 0.6650 (pp20) cc_final: 0.6263 (pp20) REVERT: A 438 HIS cc_start: 0.6365 (m90) cc_final: 0.5345 (m90) REVERT: B 250 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: D 461 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6787 (mp10) REVERT: D 491 ASP cc_start: 0.8592 (m-30) cc_final: 0.8266 (t0) REVERT: E 464 ASP cc_start: 0.8634 (m-30) cc_final: 0.8366 (m-30) REVERT: F 366 MET cc_start: 0.7589 (mtm) cc_final: 0.7340 (mtm) REVERT: F 397 ASN cc_start: 0.8142 (t0) cc_final: 0.7425 (t0) outliers start: 29 outliers final: 15 residues processed: 130 average time/residue: 0.0975 time to fit residues: 20.9210 Evaluate side-chains 125 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 THR 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 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 381 MET 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 363 LEU Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 8.9990 chunk 194 optimal weight: 0.8980 chunk 192 optimal weight: 0.5980 chunk 97 optimal weight: 40.0000 chunk 6 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 222 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 161 optimal weight: 0.0570 chunk 57 optimal weight: 40.0000 chunk 158 optimal weight: 0.0040 overall best weight: 0.4910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 ASN E 449 GLN F 342 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.105536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.070285 restraints weight = 50689.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.072947 restraints weight = 20997.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.074649 restraints weight = 12965.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.075664 restraints weight = 9915.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076203 restraints weight = 8489.336| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17389 Z= 0.091 Angle : 0.457 11.882 23723 Z= 0.250 Chirality : 0.041 0.175 2776 Planarity : 0.003 0.064 3058 Dihedral : 10.852 89.770 2750 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 1.69 % Allowed : 18.22 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.18), residues: 2340 helix: 1.27 (0.19), residues: 838 sheet: -0.68 (0.30), residues: 311 loop : -1.87 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.015 0.001 TYR A 388 PHE 0.018 0.001 PHE F 358 TRP 0.029 0.001 TRP A 354 HIS 0.009 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00191 (17389) covalent geometry : angle 0.45674 (23723) hydrogen bonds : bond 0.02552 ( 622) hydrogen bonds : angle 4.67690 ( 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 146 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 443 GLU cc_start: 0.6685 (pp20) cc_final: 0.6284 (pp20) REVERT: A 438 HIS cc_start: 0.6263 (m90) cc_final: 0.5263 (m90) REVERT: D 248 VAL cc_start: 0.8812 (t) cc_final: 0.8601 (m) REVERT: D 491 ASP cc_start: 0.8528 (m-30) cc_final: 0.8223 (t0) REVERT: E 464 ASP cc_start: 0.8579 (m-30) cc_final: 0.8327 (m-30) REVERT: F 366 MET cc_start: 0.7444 (mtm) cc_final: 0.7201 (mtm) REVERT: F 397 ASN cc_start: 0.7999 (t0) cc_final: 0.7195 (t0) outliers start: 24 outliers final: 15 residues processed: 139 average time/residue: 0.0930 time to fit residues: 21.3402 Evaluate side-chains 129 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 401 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 354 TRP 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: 0.4980 chunk 215 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 187 optimal weight: 0.6980 chunk 49 optimal weight: 50.0000 chunk 158 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 145 optimal weight: 50.0000 chunk 191 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 397 ASN D 461 GLN E 449 GLN ** F 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** 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 = 0.4027 r_free = 0.4027 target = 0.105135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.069575 restraints weight = 51351.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072261 restraints weight = 21459.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.073951 restraints weight = 13294.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.074999 restraints weight = 10134.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.075512 restraints weight = 8643.472| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17389 Z= 0.107 Angle : 0.465 12.386 23723 Z= 0.254 Chirality : 0.041 0.274 2776 Planarity : 0.003 0.066 3058 Dihedral : 10.780 88.624 2750 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.55 % Allowed : 18.29 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.18), residues: 2340 helix: 1.35 (0.19), residues: 834 sheet: -0.69 (0.30), residues: 315 loop : -1.87 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.014 0.001 TYR A 388 PHE 0.034 0.001 PHE F 250 TRP 0.029 0.002 TRP A 354 HIS 0.010 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00238 (17389) covalent geometry : angle 0.46501 (23723) hydrogen bonds : bond 0.02626 ( 622) hydrogen bonds : angle 4.62517 ( 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 136 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: C 443 GLU cc_start: 0.6679 (pp20) cc_final: 0.6274 (pp20) REVERT: A 438 HIS cc_start: 0.6292 (m90) cc_final: 0.5285 (m90) REVERT: B 250 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: D 248 VAL cc_start: 0.8819 (t) cc_final: 0.8602 (m) REVERT: D 461 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6805 (mp10) REVERT: D 491 ASP cc_start: 0.8489 (m-30) cc_final: 0.8224 (t0) REVERT: E 449 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: E 464 ASP cc_start: 0.8575 (m-30) cc_final: 0.8334 (m-30) REVERT: F 397 ASN cc_start: 0.8002 (t0) cc_final: 0.7231 (t0) outliers start: 22 outliers final: 14 residues processed: 130 average time/residue: 0.1007 time to fit residues: 21.5016 Evaluate side-chains 127 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 401 MET 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 B residue 401 MET Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 449 GLN 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: 50.0000 chunk 142 optimal weight: 50.0000 chunk 85 optimal weight: 0.9990 chunk 51 optimal weight: 40.0000 chunk 105 optimal weight: 0.0980 chunk 12 optimal weight: 40.0000 chunk 133 optimal weight: 0.4980 chunk 193 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 217 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 397 ASN E 449 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.105259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.070083 restraints weight = 51064.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072768 restraints weight = 21287.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.074494 restraints weight = 13119.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.075524 restraints weight = 9990.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.076060 restraints weight = 8518.940| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17389 Z= 0.097 Angle : 0.469 13.345 23723 Z= 0.255 Chirality : 0.041 0.253 2776 Planarity : 0.003 0.061 3058 Dihedral : 10.720 89.078 2750 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.55 % Allowed : 18.29 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.18), residues: 2340 helix: 1.37 (0.19), residues: 834 sheet: -0.63 (0.30), residues: 315 loop : -1.84 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.014 0.001 TYR A 388 PHE 0.016 0.001 PHE B 490 TRP 0.026 0.001 TRP A 354 HIS 0.008 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00206 (17389) covalent geometry : angle 0.46911 (23723) hydrogen bonds : bond 0.02580 ( 622) hydrogen bonds : angle 4.62770 ( 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 137 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 443 GLU cc_start: 0.6682 (pp20) cc_final: 0.6270 (pp20) REVERT: A 429 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7703 (p) REVERT: A 438 HIS cc_start: 0.6239 (m90) cc_final: 0.5255 (m90) REVERT: B 250 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: D 248 VAL cc_start: 0.8751 (t) cc_final: 0.8463 (p) REVERT: D 491 ASP cc_start: 0.8476 (m-30) cc_final: 0.8188 (t70) REVERT: F 381 MET cc_start: 0.9038 (mtm) cc_final: 0.8688 (mtp) REVERT: F 397 ASN cc_start: 0.7931 (t0) cc_final: 0.7202 (t0) outliers start: 22 outliers final: 15 residues processed: 129 average time/residue: 0.0911 time to fit residues: 19.2661 Evaluate side-chains 127 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 401 MET Chi-restraints excluded: chain A residue 419 ILE 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 B residue 401 MET Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 50 optimal weight: 50.0000 chunk 100 optimal weight: 50.0000 chunk 127 optimal weight: 0.3980 chunk 75 optimal weight: 6.9990 chunk 48 optimal weight: 50.0000 chunk 145 optimal weight: 50.0000 chunk 218 optimal weight: 4.9990 chunk 97 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN F 342 GLN ** F 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.105598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.069729 restraints weight = 51056.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.072322 restraints weight = 22071.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.073915 restraints weight = 13977.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.074863 restraints weight = 10897.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.075392 restraints weight = 9482.263| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17389 Z= 0.252 Angle : 0.589 13.059 23723 Z= 0.316 Chirality : 0.045 0.232 2776 Planarity : 0.003 0.056 3058 Dihedral : 11.073 85.336 2750 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 1.62 % Allowed : 18.22 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.18), residues: 2340 helix: 1.09 (0.19), residues: 842 sheet: -0.94 (0.28), residues: 338 loop : -1.91 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 286 TYR 0.013 0.002 TYR C 258 PHE 0.022 0.002 PHE F 250 TRP 0.028 0.002 TRP C 354 HIS 0.011 0.001 HIS D 438 Details of bonding type rmsd covalent geometry : bond 0.00586 (17389) covalent geometry : angle 0.58896 (23723) hydrogen bonds : bond 0.03604 ( 622) hydrogen bonds : angle 4.93201 ( 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 130 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: C 443 GLU cc_start: 0.6780 (pp20) cc_final: 0.6427 (pp20) REVERT: A 402 MET cc_start: 0.7919 (ttt) cc_final: 0.7378 (tpt) REVERT: A 429 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7939 (p) REVERT: A 438 HIS cc_start: 0.6473 (m90) cc_final: 0.5428 (m90) REVERT: B 511 PRO cc_start: 0.7444 (Cg_exo) cc_final: 0.7198 (Cg_endo) REVERT: E 252 GLN cc_start: 0.7110 (pm20) cc_final: 0.6400 (pm20) REVERT: E 464 ASP cc_start: 0.8557 (m-30) cc_final: 0.8315 (m-30) REVERT: F 381 MET cc_start: 0.9118 (mtm) cc_final: 0.8755 (mtp) REVERT: F 397 ASN cc_start: 0.8048 (t0) cc_final: 0.7358 (t0) outliers start: 23 outliers final: 18 residues processed: 124 average time/residue: 0.1026 time to fit residues: 20.9745 Evaluate side-chains 116 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 401 MET Chi-restraints excluded: chain A residue 419 ILE 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 318 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 137 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 54 optimal weight: 50.0000 chunk 218 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 51 optimal weight: 40.0000 chunk 32 optimal weight: 0.0870 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 HIS D 461 GLN E 449 GLN E 488 ASN F 325 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.104348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.069109 restraints weight = 51290.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.071764 restraints weight = 21345.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.073456 restraints weight = 13199.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.074408 restraints weight = 10066.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.075068 restraints weight = 8680.419| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17389 Z= 0.104 Angle : 0.487 14.255 23723 Z= 0.263 Chirality : 0.042 0.228 2776 Planarity : 0.003 0.050 3058 Dihedral : 10.902 89.336 2750 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 1.48 % Allowed : 18.79 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.18), residues: 2340 helix: 1.30 (0.19), residues: 837 sheet: -0.78 (0.30), residues: 315 loop : -1.85 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 254 TYR 0.013 0.001 TYR A 388 PHE 0.015 0.001 PHE B 490 TRP 0.024 0.002 TRP A 354 HIS 0.010 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00225 (17389) covalent geometry : angle 0.48715 (23723) hydrogen bonds : bond 0.02655 ( 622) hydrogen bonds : angle 4.74542 ( 1770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3286.05 seconds wall clock time: 56 minutes 59.83 seconds (3419.83 seconds total)