Starting phenix.real_space_refine on Tue Aug 26 12:30:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgs_43223/08_2025/8vgs_43223_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgs_43223/08_2025/8vgs_43223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vgs_43223/08_2025/8vgs_43223_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgs_43223/08_2025/8vgs_43223_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vgs_43223/08_2025/8vgs_43223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgs_43223/08_2025/8vgs_43223.map" } resolution = 2.14 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= -0.000 sd= 0.089 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 20 5.49 5 Mg 20 5.21 5 S 180 5.16 5 C 23480 2.51 5 N 6180 2.21 5 O 7217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.04s 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: 37097 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3660 Classifications: {'peptide': 468} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 444} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3660 Classifications: {'peptide': 468} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 444} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3660 Classifications: {'peptide': 468} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 444} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3660 Classifications: {'peptide': 468} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 444} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3660 Classifications: {'peptide': 468} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 444} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3660 Classifications: {'peptide': 468} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 444} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3660 Classifications: {'peptide': 468} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 444} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3660 Classifications: {'peptide': 468} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 444} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3660 Classifications: {'peptide': 468} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 444} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3660 Classifications: {'peptide': 468} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 444} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {' MG': 3, 'CAP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {' MG': 3, 'CAP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {' MG': 2, 'CAP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {' MG': 2, 'CAP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {' MG': 2, 'CAP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {' MG': 3, 'CAP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {' MG': 2, 'CAP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Time building chain proxies: 9.36, per 1000 atoms: 0.25 Number of scatterers: 37097 At special positions: 0 Unit cell: (173.25, 165.9, 103.95, 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 180 16.00 P 20 15.00 Mg 20 11.99 O 7217 8.00 N 6180 7.00 C 23480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 476.8 nanoseconds 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8560 Finding SS restraints... Secondary structure from input PDB file: 241 helices and 28 sheets defined 50.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 7 through 13 Processing helix chain 'A' and resid 14 through 19 removed outlier: 3.709A pdb=" N GLY A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 60 Processing helix chain 'A' and resid 71 through 77 removed outlier: 3.565A pdb=" N GLU A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.785A pdb=" N ILE A 109 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 134 through 140 removed outlier: 3.836A pdb=" N GLN A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 174 through 188 Processing helix chain 'A' and resid 206 through 226 Processing helix chain 'A' and resid 239 through 252 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 306 through 318 Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.661A pdb=" N ASP A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 407 through 416 Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.982A pdb=" N ALA A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'A' and resid 462 through 473 Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 14 through 19 removed outlier: 3.698A pdb=" N GLY B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 60 Processing helix chain 'B' and resid 71 through 77 removed outlier: 3.559A pdb=" N GLU B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET B 77 " --> pdb=" O PHE B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.836A pdb=" N ILE B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 134 through 140 removed outlier: 3.856A pdb=" N GLN B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 174 through 188 Processing helix chain 'B' and resid 206 through 226 Processing helix chain 'B' and resid 239 through 252 Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 270 through 281 Processing helix chain 'B' and resid 293 through 298 Processing helix chain 'B' and resid 306 through 318 Processing helix chain 'B' and resid 335 through 348 removed outlier: 3.673A pdb=" N ASP B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 379 Processing helix chain 'B' and resid 404 through 406 No H-bonds generated for 'chain 'B' and resid 404 through 406' Processing helix chain 'B' and resid 407 through 416 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 433 through 452 removed outlier: 4.002A pdb=" N ALA B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 462 through 473 Processing helix chain 'C' and resid 8 through 13 Processing helix chain 'C' and resid 14 through 19 removed outlier: 3.779A pdb=" N GLY C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.684A pdb=" N MET C 77 " --> pdb=" O PHE C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 105 through 114 removed outlier: 3.745A pdb=" N ILE C 109 " --> pdb=" O ASN C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 134 through 140 removed outlier: 3.887A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 174 through 188 Processing helix chain 'C' and resid 206 through 226 Processing helix chain 'C' and resid 239 through 252 Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 293 through 298 Processing helix chain 'C' and resid 306 through 318 Processing helix chain 'C' and resid 335 through 348 removed outlier: 3.595A pdb=" N ASP C 339 " --> pdb=" O SER C 335 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 379 Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 407 through 416 Processing helix chain 'C' and resid 425 through 430 Processing helix chain 'C' and resid 433 through 452 removed outlier: 3.990A pdb=" N ALA C 437 " --> pdb=" O LYS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 462 through 473 Processing helix chain 'D' and resid 8 through 12 Processing helix chain 'D' and resid 14 through 19 removed outlier: 3.759A pdb=" N GLY D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 60 Processing helix chain 'D' and resid 71 through 77 removed outlier: 3.733A pdb=" N MET D 77 " --> pdb=" O PHE D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 105 through 114 removed outlier: 3.751A pdb=" N ILE D 109 " --> pdb=" O ASN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 174 through 188 Processing helix chain 'D' and resid 206 through 226 Processing helix chain 'D' and resid 239 through 252 Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.503A pdb=" N VAL D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 306 through 318 Processing helix chain 'D' and resid 335 through 348 removed outlier: 3.622A pdb=" N ASP D 339 " --> pdb=" O SER D 335 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 379 Processing helix chain 'D' and resid 404 through 406 No H-bonds generated for 'chain 'D' and resid 404 through 406' Processing helix chain 'D' and resid 407 through 416 Processing helix chain 'D' and resid 425 through 430 Processing helix chain 'D' and resid 434 through 452 Processing helix chain 'D' and resid 454 through 459 Processing helix chain 'D' and resid 462 through 473 Processing helix chain 'E' and resid 8 through 13 removed outlier: 3.571A pdb=" N LEU E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 19 removed outlier: 3.743A pdb=" N GLY E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 71 through 77 removed outlier: 3.663A pdb=" N MET E 77 " --> pdb=" O PHE E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 105 through 114 removed outlier: 3.764A pdb=" N ILE E 109 " --> pdb=" O ASN E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 174 through 188 Processing helix chain 'E' and resid 206 through 226 Processing helix chain 'E' and resid 239 through 252 Processing helix chain 'E' and resid 266 through 270 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 293 through 298 Processing helix chain 'E' and resid 306 through 318 Processing helix chain 'E' and resid 335 through 348 removed outlier: 3.637A pdb=" N ASP E 339 " --> pdb=" O SER E 335 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL E 341 " --> pdb=" O GLU E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 379 Processing helix chain 'E' and resid 387 through 391 removed outlier: 3.721A pdb=" N GLY E 391 " --> pdb=" O SER E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 406 No H-bonds generated for 'chain 'E' and resid 404 through 406' Processing helix chain 'E' and resid 407 through 416 Processing helix chain 'E' and resid 425 through 430 Processing helix chain 'E' and resid 434 through 452 Processing helix chain 'E' and resid 454 through 459 Processing helix chain 'E' and resid 462 through 473 Processing helix chain 'F' and resid 8 through 13 Processing helix chain 'F' and resid 14 through 19 removed outlier: 3.742A pdb=" N GLY F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 60 Processing helix chain 'F' and resid 71 through 77 removed outlier: 3.674A pdb=" N MET F 77 " --> pdb=" O PHE F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 105 through 114 removed outlier: 3.707A pdb=" N ILE F 109 " --> pdb=" O ASN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 120 Processing helix chain 'F' and resid 134 through 140 removed outlier: 3.877A pdb=" N GLN F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 174 through 188 Processing helix chain 'F' and resid 206 through 226 Processing helix chain 'F' and resid 239 through 252 Processing helix chain 'F' and resid 266 through 270 Processing helix chain 'F' and resid 270 through 281 Processing helix chain 'F' and resid 293 through 298 Processing helix chain 'F' and resid 306 through 318 Processing helix chain 'F' and resid 335 through 348 removed outlier: 3.541A pdb=" N ASP F 339 " --> pdb=" O SER F 335 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL F 341 " --> pdb=" O GLU F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 379 Processing helix chain 'F' and resid 404 through 406 No H-bonds generated for 'chain 'F' and resid 404 through 406' Processing helix chain 'F' and resid 407 through 416 Processing helix chain 'F' and resid 425 through 430 Processing helix chain 'F' and resid 433 through 452 removed outlier: 4.014A pdb=" N ALA F 437 " --> pdb=" O LYS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 459 Processing helix chain 'F' and resid 462 through 473 Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 14 through 19 removed outlier: 3.716A pdb=" N GLY G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 60 Processing helix chain 'G' and resid 71 through 77 removed outlier: 3.700A pdb=" N MET G 77 " --> pdb=" O PHE G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 105 through 114 removed outlier: 3.764A pdb=" N ILE G 109 " --> pdb=" O ASN G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 120 Processing helix chain 'G' and resid 134 through 139 Processing helix chain 'G' and resid 147 through 156 Processing helix chain 'G' and resid 174 through 188 Processing helix chain 'G' and resid 206 through 226 Processing helix chain 'G' and resid 239 through 252 Processing helix chain 'G' and resid 270 through 281 removed outlier: 3.522A pdb=" N VAL G 274 " --> pdb=" O GLY G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 298 Processing helix chain 'G' and resid 306 through 318 Processing helix chain 'G' and resid 335 through 348 removed outlier: 3.680A pdb=" N ASP G 339 " --> pdb=" O SER G 335 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 379 Processing helix chain 'G' and resid 387 through 391 removed outlier: 3.718A pdb=" N GLY G 391 " --> pdb=" O SER G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 406 No H-bonds generated for 'chain 'G' and resid 404 through 406' Processing helix chain 'G' and resid 407 through 416 removed outlier: 3.508A pdb=" N ILE G 412 " --> pdb=" O LEU G 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 430 Processing helix chain 'G' and resid 433 through 452 removed outlier: 3.986A pdb=" N ALA G 437 " --> pdb=" O LYS G 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 454 through 459 Processing helix chain 'G' and resid 462 through 473 Processing helix chain 'H' and resid 8 through 13 removed outlier: 3.562A pdb=" N LEU H 13 " --> pdb=" O LEU H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 19 removed outlier: 3.744A pdb=" N GLY H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 60 Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.652A pdb=" N MET H 77 " --> pdb=" O PHE H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 105 through 114 removed outlier: 3.757A pdb=" N ILE H 109 " --> pdb=" O ASN H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 120 Processing helix chain 'H' and resid 134 through 139 Processing helix chain 'H' and resid 147 through 156 Processing helix chain 'H' and resid 174 through 188 Processing helix chain 'H' and resid 206 through 226 Processing helix chain 'H' and resid 239 through 252 Processing helix chain 'H' and resid 266 through 270 Processing helix chain 'H' and resid 270 through 281 Processing helix chain 'H' and resid 293 through 298 Processing helix chain 'H' and resid 306 through 318 Processing helix chain 'H' and resid 335 through 348 removed outlier: 3.694A pdb=" N ASP H 339 " --> pdb=" O SER H 335 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL H 341 " --> pdb=" O GLU H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 379 Processing helix chain 'H' and resid 404 through 406 No H-bonds generated for 'chain 'H' and resid 404 through 406' Processing helix chain 'H' and resid 407 through 416 Processing helix chain 'H' and resid 425 through 430 Processing helix chain 'H' and resid 434 through 452 Processing helix chain 'H' and resid 454 through 459 Processing helix chain 'H' and resid 462 through 473 Processing helix chain 'I' and resid 8 through 12 Processing helix chain 'I' and resid 14 through 19 removed outlier: 3.708A pdb=" N GLY I 19 " --> pdb=" O ILE I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 60 Processing helix chain 'I' and resid 71 through 77 removed outlier: 3.681A pdb=" N MET I 77 " --> pdb=" O PHE I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'I' and resid 105 through 114 removed outlier: 3.711A pdb=" N ILE I 109 " --> pdb=" O ASN I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 120 Processing helix chain 'I' and resid 134 through 140 removed outlier: 3.909A pdb=" N GLN I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 156 Processing helix chain 'I' and resid 174 through 188 Processing helix chain 'I' and resid 206 through 226 Processing helix chain 'I' and resid 239 through 252 Processing helix chain 'I' and resid 266 through 270 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 293 through 298 Processing helix chain 'I' and resid 306 through 318 Processing helix chain 'I' and resid 335 through 348 removed outlier: 3.517A pdb=" N ASP I 339 " --> pdb=" O SER I 335 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL I 341 " --> pdb=" O GLU I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 367 through 379 Processing helix chain 'I' and resid 404 through 406 No H-bonds generated for 'chain 'I' and resid 404 through 406' Processing helix chain 'I' and resid 407 through 416 Processing helix chain 'I' and resid 425 through 430 Processing helix chain 'I' and resid 434 through 452 Processing helix chain 'I' and resid 454 through 459 Processing helix chain 'I' and resid 462 through 473 Processing helix chain 'J' and resid 8 through 12 Processing helix chain 'J' and resid 14 through 19 removed outlier: 3.664A pdb=" N GLY J 19 " --> pdb=" O ILE J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 60 Processing helix chain 'J' and resid 71 through 77 removed outlier: 3.678A pdb=" N MET J 77 " --> pdb=" O PHE J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 100 No H-bonds generated for 'chain 'J' and resid 98 through 100' Processing helix chain 'J' and resid 105 through 114 removed outlier: 3.728A pdb=" N ILE J 109 " --> pdb=" O ASN J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 120 Processing helix chain 'J' and resid 134 through 139 Processing helix chain 'J' and resid 147 through 156 Processing helix chain 'J' and resid 174 through 188 Processing helix chain 'J' and resid 206 through 226 Processing helix chain 'J' and resid 239 through 252 Processing helix chain 'J' and resid 266 through 270 Processing helix chain 'J' and resid 270 through 281 Processing helix chain 'J' and resid 293 through 298 Processing helix chain 'J' and resid 306 through 318 Processing helix chain 'J' and resid 335 through 348 removed outlier: 3.683A pdb=" N ASP J 339 " --> pdb=" O SER J 335 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL J 341 " --> pdb=" O GLU J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 367 through 379 Processing helix chain 'J' and resid 387 through 391 removed outlier: 3.714A pdb=" N GLY J 391 " --> pdb=" O SER J 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 406 No H-bonds generated for 'chain 'J' and resid 404 through 406' Processing helix chain 'J' and resid 407 through 416 Processing helix chain 'J' and resid 425 through 430 Processing helix chain 'J' and resid 433 through 452 removed outlier: 3.984A pdb=" N ALA J 437 " --> pdb=" O LYS J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 459 Processing helix chain 'J' and resid 462 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 85 removed outlier: 5.980A pdb=" N VAL A 81 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA A 94 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN A 83 " --> pdb=" O TRP A 92 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR A 33 " --> pdb=" O TRP A 132 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP A 132 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A 35 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP A 130 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL A 37 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU A 128 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS A 39 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 126 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE A 41 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 166 removed outlier: 6.630A pdb=" N LEU A 163 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N KCX A 194 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR A 165 " --> pdb=" O KCX A 194 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 193 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASN A 234 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N HIS A 231 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU A 263 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE A 233 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASP A 265 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TYR A 260 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N HIS A 287 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE A 262 " --> pdb=" O HIS A 287 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N HIS A 289 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE A 264 " --> pdb=" O HIS A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 removed outlier: 3.573A pdb=" N GLN A 358 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 85 removed outlier: 5.982A pdb=" N VAL B 81 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN B 83 " --> pdb=" O TRP B 92 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR B 33 " --> pdb=" O TRP B 132 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TRP B 132 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B 35 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP B 130 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 37 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU B 128 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N HIS B 39 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 126 " --> pdb=" O HIS B 39 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE B 41 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 162 through 166 removed outlier: 6.604A pdb=" N LEU B 163 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N KCX B 194 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR B 165 " --> pdb=" O KCX B 194 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 193 " --> pdb=" O SER B 232 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ASN B 234 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS B 231 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B 263 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE B 233 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ASP B 265 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N TYR B 260 " --> pdb=" O PHE B 285 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N HIS B 287 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE B 262 " --> pdb=" O HIS B 287 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N HIS B 289 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE B 264 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE B 322 " --> pdb=" O ILE B 398 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 351 removed outlier: 3.564A pdb=" N GLN B 358 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 80 through 85 removed outlier: 5.974A pdb=" N VAL C 81 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA C 94 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN C 83 " --> pdb=" O TRP C 92 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR C 33 " --> pdb=" O TRP C 132 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP C 132 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU C 35 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP C 130 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 37 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU C 128 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N HIS C 39 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU C 126 " --> pdb=" O HIS C 39 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE C 41 " --> pdb=" O SER C 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 162 through 166 removed outlier: 6.597A pdb=" N LEU C 163 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N KCX C 194 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C 165 " --> pdb=" O KCX C 194 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL C 193 " --> pdb=" O SER C 232 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ASN C 234 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS C 231 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C 263 " --> pdb=" O HIS C 231 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE C 233 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ASP C 265 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR C 260 " --> pdb=" O PHE C 285 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N HIS C 287 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE C 262 " --> pdb=" O HIS C 287 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N HIS C 289 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE C 264 " --> pdb=" O HIS C 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 350 through 351 removed outlier: 3.563A pdb=" N GLN C 358 " --> pdb=" O ASP C 351 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 80 through 85 removed outlier: 6.033A pdb=" N VAL D 81 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA D 94 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN D 83 " --> pdb=" O TRP D 92 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR D 33 " --> pdb=" O TRP D 132 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP D 132 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU D 35 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP D 130 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL D 37 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU D 128 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS D 39 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 126 " --> pdb=" O HIS D 39 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE D 41 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 162 through 166 removed outlier: 6.692A pdb=" N LEU D 163 " --> pdb=" O PHE D 192 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N KCX D 194 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR D 165 " --> pdb=" O KCX D 194 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL D 193 " --> pdb=" O SER D 232 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASN D 234 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N HIS D 231 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU D 263 " --> pdb=" O HIS D 231 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE D 233 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASP D 265 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N TYR D 260 " --> pdb=" O PHE D 285 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N HIS D 287 " --> pdb=" O TYR D 260 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE D 262 " --> pdb=" O HIS D 287 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS D 289 " --> pdb=" O PHE D 262 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE D 264 " --> pdb=" O HIS D 289 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS D 323 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE D 322 " --> pdb=" O ILE D 398 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N SER D 400 " --> pdb=" O ILE D 322 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 350 through 351 removed outlier: 3.571A pdb=" N GLN D 358 " --> pdb=" O ASP D 351 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 80 through 85 removed outlier: 5.969A pdb=" N VAL E 81 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA E 94 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN E 83 " --> pdb=" O TRP E 92 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR E 33 " --> pdb=" O TRP E 132 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TRP E 132 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU E 35 " --> pdb=" O ASP E 130 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP E 130 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL E 37 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU E 128 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N HIS E 39 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU E 126 " --> pdb=" O HIS E 39 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE E 41 " --> pdb=" O SER E 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 162 through 166 removed outlier: 6.672A pdb=" N LEU E 163 " --> pdb=" O PHE E 192 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N KCX E 194 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR E 165 " --> pdb=" O KCX E 194 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 193 " --> pdb=" O SER E 232 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ASN E 234 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS E 231 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU E 263 " --> pdb=" O HIS E 231 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE E 233 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASP E 265 " --> pdb=" O PHE E 233 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N TYR E 260 " --> pdb=" O PHE E 285 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N HIS E 287 " --> pdb=" O TYR E 260 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE E 262 " --> pdb=" O HIS E 287 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N HIS E 289 " --> pdb=" O PHE E 262 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE E 264 " --> pdb=" O HIS E 289 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 350 through 351 removed outlier: 3.517A pdb=" N GLN E 358 " --> pdb=" O ASP E 351 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 80 through 85 removed outlier: 5.984A pdb=" N VAL F 81 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA F 94 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN F 83 " --> pdb=" O TRP F 92 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR F 33 " --> pdb=" O TRP F 132 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP F 132 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU F 35 " --> pdb=" O ASP F 130 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASP F 130 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL F 37 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU F 128 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N HIS F 39 " --> pdb=" O LEU F 126 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 126 " --> pdb=" O HIS F 39 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE F 41 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N GLY F 304 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU F 126 " --> pdb=" O GLY F 304 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 162 through 166 removed outlier: 6.678A pdb=" N LEU F 163 " --> pdb=" O PHE F 192 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N KCX F 194 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR F 165 " --> pdb=" O KCX F 194 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL F 193 " --> pdb=" O SER F 232 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ASN F 234 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS F 231 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU F 263 " --> pdb=" O HIS F 231 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE F 233 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASP F 265 " --> pdb=" O PHE F 233 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N TYR F 260 " --> pdb=" O PHE F 285 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N HIS F 287 " --> pdb=" O TYR F 260 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE F 262 " --> pdb=" O HIS F 287 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N HIS F 289 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE F 264 " --> pdb=" O HIS F 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 80 through 85 removed outlier: 6.039A pdb=" N VAL G 81 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA G 94 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN G 83 " --> pdb=" O TRP G 92 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR G 33 " --> pdb=" O TRP G 132 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP G 132 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU G 35 " --> pdb=" O ASP G 130 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP G 130 " --> pdb=" O LEU G 35 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL G 37 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU G 128 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N HIS G 39 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU G 126 " --> pdb=" O HIS G 39 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE G 41 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 162 through 166 removed outlier: 6.664A pdb=" N LEU G 163 " --> pdb=" O PHE G 192 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N KCX G 194 " --> pdb=" O LEU G 163 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR G 165 " --> pdb=" O KCX G 194 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL G 193 " --> pdb=" O SER G 232 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASN G 234 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS G 231 " --> pdb=" O ALA G 261 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU G 263 " --> pdb=" O HIS G 231 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE G 233 " --> pdb=" O LEU G 263 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ASP G 265 " --> pdb=" O PHE G 233 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N TYR G 260 " --> pdb=" O PHE G 285 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N HIS G 287 " --> pdb=" O TYR G 260 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE G 262 " --> pdb=" O HIS G 287 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS G 289 " --> pdb=" O PHE G 262 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE G 264 " --> pdb=" O HIS G 289 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE G 322 " --> pdb=" O ILE G 398 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N SER G 400 " --> pdb=" O ILE G 322 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 80 through 85 removed outlier: 5.966A pdb=" N VAL H 81 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA H 94 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN H 83 " --> pdb=" O TRP H 92 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR H 33 " --> pdb=" O TRP H 132 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TRP H 132 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU H 35 " --> pdb=" O ASP H 130 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP H 130 " --> pdb=" O LEU H 35 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL H 37 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU H 128 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N HIS H 39 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU H 126 " --> pdb=" O HIS H 39 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE H 41 " --> pdb=" O SER H 124 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 162 through 166 removed outlier: 6.622A pdb=" N LEU H 163 " --> pdb=" O PHE H 192 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N KCX H 194 " --> pdb=" O LEU H 163 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR H 165 " --> pdb=" O KCX H 194 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL H 193 " --> pdb=" O SER H 232 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN H 234 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N HIS H 231 " --> pdb=" O ALA H 261 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU H 263 " --> pdb=" O HIS H 231 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N PHE H 233 " --> pdb=" O LEU H 263 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ASP H 265 " --> pdb=" O PHE H 233 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TYR H 260 " --> pdb=" O PHE H 285 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N HIS H 287 " --> pdb=" O TYR H 260 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE H 262 " --> pdb=" O HIS H 287 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N HIS H 289 " --> pdb=" O PHE H 262 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE H 264 " --> pdb=" O HIS H 289 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE H 322 " --> pdb=" O ILE H 398 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR H 423 " --> pdb=" O PRO H 397 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE H 399 " --> pdb=" O THR H 423 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 350 through 351 removed outlier: 3.566A pdb=" N GLN H 358 " --> pdb=" O ASP H 351 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 80 through 85 removed outlier: 5.896A pdb=" N VAL I 81 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA I 94 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN I 83 " --> pdb=" O TRP I 92 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR I 33 " --> pdb=" O TRP I 132 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP I 132 " --> pdb=" O TYR I 33 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU I 35 " --> pdb=" O ASP I 130 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP I 130 " --> pdb=" O LEU I 35 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL I 37 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU I 128 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS I 39 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU I 126 " --> pdb=" O HIS I 39 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE I 41 " --> pdb=" O SER I 124 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 162 through 166 removed outlier: 6.623A pdb=" N LEU I 163 " --> pdb=" O PHE I 192 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N KCX I 194 " --> pdb=" O LEU I 163 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR I 165 " --> pdb=" O KCX I 194 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL I 193 " --> pdb=" O SER I 232 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ASN I 234 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS I 231 " --> pdb=" O ALA I 261 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU I 263 " --> pdb=" O HIS I 231 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE I 233 " --> pdb=" O LEU I 263 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP I 265 " --> pdb=" O PHE I 233 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N TYR I 260 " --> pdb=" O PHE I 285 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N HIS I 287 " --> pdb=" O TYR I 260 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE I 262 " --> pdb=" O HIS I 287 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N HIS I 289 " --> pdb=" O PHE I 262 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE I 264 " --> pdb=" O HIS I 289 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE I 322 " --> pdb=" O ILE I 398 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 350 through 351 removed outlier: 3.501A pdb=" N GLN I 358 " --> pdb=" O ASP I 351 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 80 through 85 removed outlier: 5.890A pdb=" N VAL J 81 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA J 94 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN J 83 " --> pdb=" O TRP J 92 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR J 33 " --> pdb=" O TRP J 132 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TRP J 132 " --> pdb=" O TYR J 33 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU J 35 " --> pdb=" O ASP J 130 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP J 130 " --> pdb=" O LEU J 35 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL J 37 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU J 128 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS J 39 " --> pdb=" O LEU J 126 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU J 126 " --> pdb=" O HIS J 39 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE J 41 " --> pdb=" O SER J 124 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 162 through 166 removed outlier: 6.600A pdb=" N LEU J 163 " --> pdb=" O PHE J 192 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N KCX J 194 " --> pdb=" O LEU J 163 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR J 165 " --> pdb=" O KCX J 194 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL J 193 " --> pdb=" O SER J 232 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASN J 234 " --> pdb=" O VAL J 193 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N HIS J 231 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU J 263 " --> pdb=" O HIS J 231 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE J 233 " --> pdb=" O LEU J 263 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ASP J 265 " --> pdb=" O PHE J 233 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TYR J 260 " --> pdb=" O PHE J 285 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N HIS J 287 " --> pdb=" O TYR J 260 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE J 262 " --> pdb=" O HIS J 287 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N HIS J 289 " --> pdb=" O PHE J 262 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE J 264 " --> pdb=" O HIS J 289 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE J 322 " --> pdb=" O ILE J 398 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 350 through 351 1593 hydrogen bonds defined for protein. 4590 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: 7.76 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11998 1.34 - 1.46: 8659 1.46 - 1.58: 16692 1.58 - 1.70: 21 1.70 - 1.81: 300 Bond restraints: 37670 Sorted by residual: bond pdb=" NZ KCX B 194 " pdb=" CX KCX B 194 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" NZ KCX C 194 " pdb=" CX KCX C 194 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" NZ KCX A 194 " pdb=" CX KCX A 194 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" NZ KCX J 194 " pdb=" CX KCX J 194 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" NZ KCX I 194 " pdb=" CX KCX I 194 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 37665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 50750 2.76 - 5.52: 237 5.52 - 8.28: 41 8.28 - 11.04: 2 11.04 - 13.80: 20 Bond angle restraints: 51050 Sorted by residual: angle pdb=" C LYS H 352 " pdb=" N GLY H 353 " pdb=" CA GLY H 353 " ideal model delta sigma weight residual 121.70 135.50 -13.80 1.80e+00 3.09e-01 5.88e+01 angle pdb=" C LYS E 352 " pdb=" N GLY E 353 " pdb=" CA GLY E 353 " ideal model delta sigma weight residual 121.70 135.45 -13.75 1.80e+00 3.09e-01 5.84e+01 angle pdb=" C LYS B 352 " pdb=" N GLY B 353 " pdb=" CA GLY B 353 " ideal model delta sigma weight residual 121.70 135.40 -13.70 1.80e+00 3.09e-01 5.79e+01 angle pdb=" C LYS J 352 " pdb=" N GLY J 353 " pdb=" CA GLY J 353 " ideal model delta sigma weight residual 121.70 135.39 -13.69 1.80e+00 3.09e-01 5.79e+01 angle pdb=" C LYS A 352 " pdb=" N GLY A 353 " pdb=" CA GLY A 353 " ideal model delta sigma weight residual 121.70 135.35 -13.65 1.80e+00 3.09e-01 5.75e+01 ... (remaining 51045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.29: 21364 33.29 - 66.59: 772 66.59 - 99.88: 82 99.88 - 133.17: 12 133.17 - 166.46: 10 Dihedral angle restraints: 22240 sinusoidal: 8850 harmonic: 13390 Sorted by residual: dihedral pdb=" C3 CAP C 503 " pdb=" C CAP C 503 " pdb=" C2 CAP C 503 " pdb=" O6 CAP C 503 " ideal model delta sinusoidal sigma weight residual 81.86 -84.60 166.46 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C3 CAP E 502 " pdb=" C CAP E 502 " pdb=" C2 CAP E 502 " pdb=" O6 CAP E 502 " ideal model delta sinusoidal sigma weight residual 81.86 -83.08 164.95 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C3 CAP A 504 " pdb=" C CAP A 504 " pdb=" C2 CAP A 504 " pdb=" O6 CAP A 504 " ideal model delta sinusoidal sigma weight residual 81.86 -78.88 160.74 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 22237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3742 0.035 - 0.069: 1191 0.069 - 0.104: 478 0.104 - 0.139: 98 0.139 - 0.173: 11 Chirality restraints: 5520 Sorted by residual: chirality pdb=" CA GLU G 197 " pdb=" N GLU G 197 " pdb=" C GLU G 197 " pdb=" CB GLU G 197 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CA GLU D 197 " pdb=" N GLU D 197 " pdb=" C GLU D 197 " pdb=" CB GLU D 197 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CA GLU I 197 " pdb=" N GLU I 197 " pdb=" C GLU I 197 " pdb=" CB GLU I 197 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 5517 not shown) Planarity restraints: 6610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU I 256 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO I 257 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO I 257 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 257 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 240 " 0.013 2.00e-02 2.50e+03 1.49e-02 3.86e+00 pdb=" CG PHE J 240 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE J 240 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE J 240 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE J 240 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE J 240 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE J 240 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 409 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.83e+00 pdb=" N PRO E 410 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 410 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 410 " -0.027 5.00e-02 4.00e+02 ... (remaining 6607 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 152 2.32 - 2.96: 17230 2.96 - 3.61: 65582 3.61 - 4.25: 106277 4.25 - 4.90: 166483 Nonbonded interactions: 355724 Sorted by model distance: nonbonded pdb=" OD1 ASP B 196 " pdb="MG MG B 501 " model vdw 1.671 2.170 nonbonded pdb=" OD1 ASP J 196 " pdb="MG MG J 501 " model vdw 1.974 2.170 nonbonded pdb=" OD1 ASP F 196 " pdb="MG MG F 501 " model vdw 1.977 2.170 nonbonded pdb=" OE1 GLU E 197 " pdb="MG MG E 501 " model vdw 1.992 2.170 nonbonded pdb=" OQ2 KCX C 194 " pdb="MG MG C 501 " model vdw 1.997 2.170 ... (remaining 355719 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 501) selection = (chain 'B' and resid 7 through 501) selection = (chain 'C' and resid 7 through 501) selection = (chain 'D' and resid 7 through 501) selection = (chain 'E' and resid 7 through 501) selection = (chain 'F' and resid 7 through 501) selection = (chain 'G' and resid 7 through 501) selection = (chain 'H' and resid 7 through 501) selection = (chain 'I' and resid 7 through 501) selection = (chain 'J' and resid 7 through 501) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 35.370 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.090 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.003 0.083 37670 Z= 0.140 Angle : 0.599 13.798 51050 Z= 0.324 Chirality : 0.041 0.173 5520 Planarity : 0.004 0.052 6610 Dihedral : 17.283 166.464 13680 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.96 % Allowed : 14.23 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.67 % 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 (0.12), residues: 4630 helix: 1.41 (0.11), residues: 1980 sheet: 1.20 (0.23), residues: 460 loop : -0.15 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 246 TYR 0.018 0.002 TYR B 112 PHE 0.031 0.002 PHE J 240 TRP 0.023 0.002 TRP E 97 HIS 0.005 0.001 HIS C 293 Details of bonding type rmsd covalent geometry : bond 0.00273 (37670) covalent geometry : angle 0.59880 (51050) hydrogen bonds : bond 0.16585 ( 1593) hydrogen bonds : angle 6.77597 ( 4590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 615 time to evaluate : 1.237 Fit side-chains REVERT: A 218 MET cc_start: 0.8295 (ttm) cc_final: 0.7625 (ttm) REVERT: B 218 MET cc_start: 0.8282 (ttm) cc_final: 0.7645 (ttm) REVERT: C 151 MET cc_start: 0.8408 (ttp) cc_final: 0.8129 (ttm) REVERT: C 241 ASP cc_start: 0.8064 (m-30) cc_final: 0.7845 (m-30) REVERT: C 243 MET cc_start: 0.9090 (ttp) cc_final: 0.8884 (ttp) REVERT: C 332 MET cc_start: 0.7299 (mmt) cc_final: 0.6726 (mmt) REVERT: C 348 ARG cc_start: 0.7965 (mtt180) cc_final: 0.7734 (mtt180) REVERT: C 464 GLU cc_start: 0.6666 (mp0) cc_final: 0.6443 (mp0) REVERT: D 210 MET cc_start: 0.9184 (tmm) cc_final: 0.8812 (tmm) REVERT: D 243 MET cc_start: 0.9235 (ttp) cc_final: 0.9018 (ttp) REVERT: D 338 GLU cc_start: 0.6445 (mm-30) cc_final: 0.5979 (mm-30) REVERT: E 14 ASN cc_start: 0.8209 (p0) cc_final: 0.7960 (p0) REVERT: E 42 SER cc_start: 0.8603 (p) cc_final: 0.8381 (t) REVERT: E 46 LEU cc_start: 0.8401 (mp) cc_final: 0.8183 (mt) REVERT: E 70 GLU cc_start: 0.7927 (tt0) cc_final: 0.7463 (mt-10) REVERT: E 122 GLU cc_start: 0.7927 (mp0) cc_final: 0.7700 (mp0) REVERT: E 137 MET cc_start: 0.9021 (ttt) cc_final: 0.8795 (ttt) REVERT: E 368 LYS cc_start: 0.7554 (mmtp) cc_final: 0.7340 (mmtm) REVERT: E 373 ILE cc_start: 0.8035 (mt) cc_final: 0.7783 (mt) REVERT: E 447 GLU cc_start: 0.6088 (mm-30) cc_final: 0.5798 (pt0) REVERT: F 151 MET cc_start: 0.8415 (ttp) cc_final: 0.8177 (ttm) REVERT: F 156 ASN cc_start: 0.7508 (t0) cc_final: 0.7230 (m110) REVERT: F 332 MET cc_start: 0.7220 (mmt) cc_final: 0.6418 (mmt) REVERT: F 400 SER cc_start: 0.8654 (m) cc_final: 0.8447 (p) REVERT: F 464 GLU cc_start: 0.6716 (mp0) cc_final: 0.6498 (mp0) REVERT: G 171 MET cc_start: 0.8738 (tpp) cc_final: 0.8496 (tpp) REVERT: G 212 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.8190 (mtm-85) REVERT: G 218 MET cc_start: 0.8363 (ttm) cc_final: 0.8090 (ttm) REVERT: G 243 MET cc_start: 0.9228 (ttp) cc_final: 0.8965 (ttp) REVERT: G 338 GLU cc_start: 0.6290 (mm-30) cc_final: 0.5693 (mm-30) REVERT: H 14 ASN cc_start: 0.8207 (p0) cc_final: 0.8000 (p0) REVERT: H 42 SER cc_start: 0.8612 (p) cc_final: 0.8385 (t) REVERT: H 46 LEU cc_start: 0.8406 (mp) cc_final: 0.8186 (mt) REVERT: H 70 GLU cc_start: 0.7800 (tt0) cc_final: 0.7408 (mt-10) REVERT: H 122 GLU cc_start: 0.7927 (mp0) cc_final: 0.7700 (mp0) REVERT: H 156 ASN cc_start: 0.7786 (t0) cc_final: 0.7289 (m-40) REVERT: H 373 ILE cc_start: 0.8069 (mt) cc_final: 0.7834 (mt) REVERT: I 77 MET cc_start: 0.8869 (mmp) cc_final: 0.8669 (mmm) REVERT: I 156 ASN cc_start: 0.7630 (t0) cc_final: 0.7280 (m110) REVERT: I 187 VAL cc_start: 0.8397 (p) cc_final: 0.7776 (t) REVERT: I 256 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6885 (mp0) REVERT: I 332 MET cc_start: 0.7269 (mmt) cc_final: 0.6735 (mmt) REVERT: I 375 GLN cc_start: 0.7462 (mt0) cc_final: 0.7105 (mt0) REVERT: J 15 ILE cc_start: 0.8347 (mm) cc_final: 0.8070 (mp) REVERT: J 77 MET cc_start: 0.8878 (mmp) cc_final: 0.8632 (mmm) REVERT: J 156 ASN cc_start: 0.7717 (t0) cc_final: 0.7322 (m110) REVERT: J 243 MET cc_start: 0.9144 (ttp) cc_final: 0.8886 (ttp) REVERT: J 256 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6845 (mp0) REVERT: J 332 MET cc_start: 0.7015 (mmt) cc_final: 0.6491 (mmt) REVERT: J 375 GLN cc_start: 0.7413 (mt0) cc_final: 0.7037 (mt0) REVERT: J 417 ASN cc_start: 0.7741 (p0) cc_final: 0.7465 (p0) REVERT: J 447 GLU cc_start: 0.6298 (mm-30) cc_final: 0.6037 (pt0) outliers start: 75 outliers final: 56 residues processed: 688 average time/residue: 0.7739 time to fit residues: 637.1067 Evaluate side-chains 589 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 533 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 361 SER Chi-restraints excluded: chain F residue 455 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 361 SER Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 236 SER Chi-restraints excluded: chain I residue 335 SER Chi-restraints excluded: chain I residue 361 SER Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 236 SER Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 335 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 354 HIS A 429 HIS B 107 GLN B 354 HIS B 429 HIS C 107 GLN C 417 ASN D 16 HIS D 107 GLN D 344 GLN D 345 ASN D 354 HIS D 429 HIS E 16 HIS E 107 GLN E 429 HIS F 107 GLN F 213 ASN F 417 ASN F 429 HIS G 107 GLN G 344 GLN G 345 ASN G 354 HIS G 429 HIS H 16 HIS H 107 GLN H 333 GLN I 354 HIS J 68 ASN J 107 GLN J 354 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.171280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.135586 restraints weight = 28553.881| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.25 r_work: 0.3309 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 37670 Z= 0.255 Angle : 0.757 9.603 51050 Z= 0.412 Chirality : 0.049 0.223 5520 Planarity : 0.005 0.049 6610 Dihedral : 11.099 174.307 5202 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.87 % Allowed : 13.34 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.67 % 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: 0.57 (0.12), residues: 4630 helix: 1.19 (0.11), residues: 2020 sheet: -0.20 (0.20), residues: 600 loop : -0.16 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 160 TYR 0.028 0.004 TYR G 20 PHE 0.031 0.003 PHE D 411 TRP 0.020 0.003 TRP J 97 HIS 0.013 0.003 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00538 (37670) covalent geometry : angle 0.75721 (51050) hydrogen bonds : bond 0.05675 ( 1593) hydrogen bonds : angle 5.66177 ( 4590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 585 time to evaluate : 1.610 Fit side-chains REVERT: A 139 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: A 151 MET cc_start: 0.8195 (ttp) cc_final: 0.7987 (ttm) REVERT: A 218 MET cc_start: 0.8241 (ttm) cc_final: 0.7525 (ttm) REVERT: A 447 GLU cc_start: 0.5930 (mm-30) cc_final: 0.5343 (pt0) REVERT: B 139 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: B 218 MET cc_start: 0.8232 (ttm) cc_final: 0.7521 (ttm) REVERT: B 447 GLU cc_start: 0.5902 (mm-30) cc_final: 0.5302 (pt0) REVERT: C 166 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8259 (mp) REVERT: C 338 GLU cc_start: 0.6434 (mm-30) cc_final: 0.5571 (mm-30) REVERT: C 447 GLU cc_start: 0.5923 (mm-30) cc_final: 0.5538 (pt0) REVERT: D 42 SER cc_start: 0.8514 (p) cc_final: 0.8270 (m) REVERT: D 107 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.9024 (pp30) REVERT: D 150 ASP cc_start: 0.8292 (m-30) cc_final: 0.8016 (m-30) REVERT: D 153 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7289 (mttp) REVERT: D 338 GLU cc_start: 0.6486 (mm-30) cc_final: 0.5667 (mm-30) REVERT: D 350 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8193 (tttt) REVERT: D 351 ASP cc_start: 0.7573 (t0) cc_final: 0.7327 (t70) REVERT: E 14 ASN cc_start: 0.8273 (p0) cc_final: 0.7886 (p0) REVERT: E 70 GLU cc_start: 0.8002 (tt0) cc_final: 0.7376 (mt-10) REVERT: E 153 LYS cc_start: 0.7835 (tttt) cc_final: 0.7393 (mptp) REVERT: E 156 ASN cc_start: 0.7843 (t0) cc_final: 0.7227 (m-40) REVERT: E 166 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8205 (mp) REVERT: E 365 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.5998 (tm-30) REVERT: E 368 LYS cc_start: 0.7664 (mmtp) cc_final: 0.7435 (mmtm) REVERT: E 373 ILE cc_start: 0.7889 (mt) cc_final: 0.7646 (mt) REVERT: E 447 GLU cc_start: 0.5569 (mm-30) cc_final: 0.5171 (pt0) REVERT: F 139 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: F 156 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7413 (t0) REVERT: F 166 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8263 (mp) REVERT: F 332 MET cc_start: 0.7297 (mmt) cc_final: 0.6531 (mmt) REVERT: F 338 GLU cc_start: 0.6433 (mm-30) cc_final: 0.5543 (mm-30) REVERT: F 365 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6249 (tm-30) REVERT: F 457 GLU cc_start: 0.4407 (tm-30) cc_final: 0.4084 (tm-30) REVERT: G 42 SER cc_start: 0.8494 (p) cc_final: 0.8260 (m) REVERT: G 77 MET cc_start: 0.8643 (mmp) cc_final: 0.8352 (mmm) REVERT: G 139 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: G 150 ASP cc_start: 0.8288 (m-30) cc_final: 0.8010 (m-30) REVERT: G 171 MET cc_start: 0.8733 (tpp) cc_final: 0.8470 (tpp) REVERT: G 218 MET cc_start: 0.8296 (ttm) cc_final: 0.8027 (ttm) REVERT: G 338 GLU cc_start: 0.6478 (mm-30) cc_final: 0.5642 (mm-30) REVERT: G 351 ASP cc_start: 0.7557 (t0) cc_final: 0.7271 (t70) REVERT: G 357 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7187 (tm-30) REVERT: H 14 ASN cc_start: 0.8285 (p0) cc_final: 0.7924 (p0) REVERT: H 137 MET cc_start: 0.9118 (ttt) cc_final: 0.8881 (ttt) REVERT: H 153 LYS cc_start: 0.7855 (tttt) cc_final: 0.7408 (mptp) REVERT: H 156 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7419 (m-40) REVERT: H 373 ILE cc_start: 0.7896 (mt) cc_final: 0.7656 (mt) REVERT: I 139 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: I 156 ASN cc_start: 0.7823 (t0) cc_final: 0.7319 (m110) REVERT: I 256 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6627 (mp0) REVERT: I 332 MET cc_start: 0.7391 (mmt) cc_final: 0.6695 (mmt) REVERT: I 347 LEU cc_start: 0.7690 (tp) cc_final: 0.7397 (mt) REVERT: I 375 GLN cc_start: 0.7245 (mt0) cc_final: 0.6918 (mt0) REVERT: J 77 MET cc_start: 0.8715 (mmp) cc_final: 0.8168 (mmp) REVERT: J 156 ASN cc_start: 0.7750 (t0) cc_final: 0.7175 (m110) REVERT: J 243 MET cc_start: 0.9159 (ttp) cc_final: 0.8938 (ttp) REVERT: J 256 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6514 (mp0) REVERT: J 332 MET cc_start: 0.7470 (mmt) cc_final: 0.6902 (mmt) REVERT: J 347 LEU cc_start: 0.7768 (tp) cc_final: 0.7487 (mt) REVERT: J 375 GLN cc_start: 0.7233 (mt0) cc_final: 0.6883 (mt0) REVERT: J 417 ASN cc_start: 0.7621 (p0) cc_final: 0.7401 (p0) REVERT: J 424 MET cc_start: 0.8175 (mtt) cc_final: 0.7859 (mtm) REVERT: J 447 GLU cc_start: 0.5877 (mm-30) cc_final: 0.5426 (pt0) outliers start: 110 outliers final: 52 residues processed: 665 average time/residue: 0.7353 time to fit residues: 585.1432 Evaluate side-chains 610 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 543 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 365 GLU Chi-restraints excluded: chain E residue 400 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 156 ASN Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 455 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 156 ASN Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 400 SER Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 335 SER Chi-restraints excluded: chain I residue 400 SER Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 361 SER Chi-restraints excluded: chain J residue 400 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 391 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 359 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 441 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 373 optimal weight: 7.9990 chunk 400 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 354 HIS B 107 GLN B 354 HIS C 107 GLN C 345 ASN C 417 ASN ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS E 16 HIS E 107 GLN F 107 GLN F 345 ASN F 417 ASN G 107 GLN G 345 ASN G 354 HIS H 16 HIS ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN I 354 HIS J 68 ASN J 107 GLN J 354 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.170685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134900 restraints weight = 28585.439| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.12 r_work: 0.3294 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 37670 Z= 0.262 Angle : 0.767 10.936 51050 Z= 0.419 Chirality : 0.049 0.221 5520 Planarity : 0.005 0.048 6610 Dihedral : 10.984 174.524 5161 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.79 % Allowed : 13.89 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.67 % 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: 0.29 (0.12), residues: 4630 helix: 1.00 (0.11), residues: 2020 sheet: -0.41 (0.20), residues: 600 loop : -0.35 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 102 TYR 0.028 0.004 TYR G 20 PHE 0.032 0.003 PHE I 411 TRP 0.020 0.003 TRP H 97 HIS 0.013 0.003 HIS H 231 Details of bonding type rmsd covalent geometry : bond 0.00553 (37670) covalent geometry : angle 0.76740 (51050) hydrogen bonds : bond 0.05581 ( 1593) hydrogen bonds : angle 5.57290 ( 4590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 561 time to evaluate : 1.111 Fit side-chains REVERT: A 139 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: A 151 MET cc_start: 0.8202 (ttp) cc_final: 0.7984 (ttm) REVERT: A 218 MET cc_start: 0.8291 (ttm) cc_final: 0.7577 (ttm) REVERT: A 243 MET cc_start: 0.9220 (ttp) cc_final: 0.8902 (ttp) REVERT: A 338 GLU cc_start: 0.6842 (mm-30) cc_final: 0.5742 (mm-30) REVERT: A 447 GLU cc_start: 0.5958 (mm-30) cc_final: 0.5373 (pt0) REVERT: B 139 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: B 187 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.7910 (t) REVERT: B 218 MET cc_start: 0.8281 (ttm) cc_final: 0.7583 (ttm) REVERT: B 243 MET cc_start: 0.9179 (ttp) cc_final: 0.8883 (ttp) REVERT: B 447 GLU cc_start: 0.5912 (mm-30) cc_final: 0.5329 (pt0) REVERT: C 166 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8209 (mp) REVERT: C 338 GLU cc_start: 0.6457 (mm-30) cc_final: 0.5566 (mm-30) REVERT: C 348 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7793 (mtt180) REVERT: C 447 GLU cc_start: 0.5940 (mm-30) cc_final: 0.5558 (pt0) REVERT: C 457 GLU cc_start: 0.4212 (tm-30) cc_final: 0.3880 (tm-30) REVERT: D 150 ASP cc_start: 0.8327 (m-30) cc_final: 0.8028 (m-30) REVERT: D 153 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7251 (mttp) REVERT: D 338 GLU cc_start: 0.6540 (mm-30) cc_final: 0.5734 (mm-30) REVERT: D 350 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8228 (tttp) REVERT: D 357 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: E 70 GLU cc_start: 0.8014 (tt0) cc_final: 0.7383 (mt-10) REVERT: E 139 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: E 153 LYS cc_start: 0.7907 (tttt) cc_final: 0.7449 (mptp) REVERT: E 156 ASN cc_start: 0.7863 (t0) cc_final: 0.7245 (m-40) REVERT: E 166 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8245 (mp) REVERT: E 365 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6040 (tm-30) REVERT: E 373 ILE cc_start: 0.7917 (mt) cc_final: 0.7695 (mt) REVERT: E 447 GLU cc_start: 0.5558 (mm-30) cc_final: 0.5258 (pt0) REVERT: F 139 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: F 166 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8229 (mp) REVERT: F 332 MET cc_start: 0.7344 (mmt) cc_final: 0.6884 (mmt) REVERT: F 338 GLU cc_start: 0.6315 (mm-30) cc_final: 0.5426 (mm-30) REVERT: F 365 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6290 (tm-30) REVERT: F 457 GLU cc_start: 0.4174 (tm-30) cc_final: 0.3843 (tm-30) REVERT: G 139 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: G 150 ASP cc_start: 0.8304 (m-30) cc_final: 0.8003 (m-30) REVERT: G 171 MET cc_start: 0.8779 (tpp) cc_final: 0.8553 (tpp) REVERT: G 218 MET cc_start: 0.8333 (ttm) cc_final: 0.8044 (ttm) REVERT: G 338 GLU cc_start: 0.6550 (mm-30) cc_final: 0.5741 (mm-30) REVERT: H 14 ASN cc_start: 0.8272 (p0) cc_final: 0.7882 (p0) REVERT: H 137 MET cc_start: 0.9169 (ttt) cc_final: 0.8922 (ttt) REVERT: H 139 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: H 153 LYS cc_start: 0.7915 (tttt) cc_final: 0.7453 (mptp) REVERT: H 156 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7442 (m-40) REVERT: H 166 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8174 (mp) REVERT: H 338 GLU cc_start: 0.6303 (mm-30) cc_final: 0.5461 (mm-30) REVERT: I 139 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7856 (tm-30) REVERT: I 156 ASN cc_start: 0.7848 (t0) cc_final: 0.7294 (m110) REVERT: I 256 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6741 (mp0) REVERT: I 332 MET cc_start: 0.7500 (mmt) cc_final: 0.7121 (mmt) REVERT: I 347 LEU cc_start: 0.7900 (tp) cc_final: 0.7570 (mt) REVERT: I 375 GLN cc_start: 0.7327 (mt0) cc_final: 0.6997 (mt0) REVERT: J 77 MET cc_start: 0.8758 (mmp) cc_final: 0.8529 (mmm) REVERT: J 156 ASN cc_start: 0.7772 (t0) cc_final: 0.7202 (m110) REVERT: J 243 MET cc_start: 0.9151 (ttp) cc_final: 0.8911 (ttp) REVERT: J 256 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6692 (mp0) REVERT: J 332 MET cc_start: 0.7493 (mmt) cc_final: 0.7211 (mmt) REVERT: J 347 LEU cc_start: 0.7970 (tp) cc_final: 0.7663 (mt) REVERT: J 424 MET cc_start: 0.8082 (mtt) cc_final: 0.7771 (mtm) REVERT: J 447 GLU cc_start: 0.5891 (mm-30) cc_final: 0.5478 (pt0) outliers start: 107 outliers final: 55 residues processed: 640 average time/residue: 0.7839 time to fit residues: 598.6368 Evaluate side-chains 615 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 542 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 365 GLU Chi-restraints excluded: chain E residue 400 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 455 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 361 SER Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 156 ASN Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 400 SER Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 335 SER Chi-restraints excluded: chain I residue 400 SER Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 400 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 60 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 246 optimal weight: 3.9990 chunk 352 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 392 optimal weight: 6.9990 chunk 361 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 308 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 354 HIS B 107 GLN B 354 HIS C 107 GLN C 417 ASN D 107 GLN D 333 GLN D 345 ASN E 16 HIS E 107 GLN E 333 GLN F 107 GLN F 417 ASN G 107 GLN G 345 ASN G 354 HIS H 16 HIS H 107 GLN I 354 HIS J 68 ASN J 107 GLN J 354 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.172842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.135276 restraints weight = 28811.204| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.13 r_work: 0.3333 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37670 Z= 0.168 Angle : 0.651 8.820 51050 Z= 0.353 Chirality : 0.045 0.176 5520 Planarity : 0.004 0.046 6610 Dihedral : 10.363 172.313 5161 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.64 % Allowed : 14.36 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.67 % 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: 0.54 (0.12), residues: 4630 helix: 1.32 (0.11), residues: 2020 sheet: -0.45 (0.20), residues: 600 loop : -0.27 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 279 TYR 0.019 0.003 TYR G 20 PHE 0.029 0.002 PHE F 411 TRP 0.018 0.002 TRP E 97 HIS 0.007 0.002 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00349 (37670) covalent geometry : angle 0.65076 (51050) hydrogen bonds : bond 0.04608 ( 1593) hydrogen bonds : angle 5.28842 ( 4590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 576 time to evaluate : 1.206 Fit side-chains REVERT: A 139 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: A 218 MET cc_start: 0.8252 (ttm) cc_final: 0.7567 (ttm) REVERT: A 337 GLU cc_start: 0.6376 (mp0) cc_final: 0.6126 (mp0) REVERT: A 338 GLU cc_start: 0.6771 (mm-30) cc_final: 0.5672 (mm-30) REVERT: A 447 GLU cc_start: 0.5836 (mm-30) cc_final: 0.5308 (pt0) REVERT: B 139 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: B 151 MET cc_start: 0.8452 (ttm) cc_final: 0.8214 (ttm) REVERT: B 187 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7955 (t) REVERT: B 218 MET cc_start: 0.8252 (ttm) cc_final: 0.7571 (ttm) REVERT: B 243 MET cc_start: 0.9161 (ttp) cc_final: 0.8870 (ttp) REVERT: B 256 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: B 338 GLU cc_start: 0.6776 (mm-30) cc_final: 0.5702 (mm-30) REVERT: B 447 GLU cc_start: 0.5792 (mm-30) cc_final: 0.5258 (pt0) REVERT: C 156 ASN cc_start: 0.7687 (t0) cc_final: 0.7155 (m-40) REVERT: C 166 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8175 (mp) REVERT: C 338 GLU cc_start: 0.6471 (mm-30) cc_final: 0.5454 (mm-30) REVERT: C 424 MET cc_start: 0.8013 (mtt) cc_final: 0.7671 (mtm) REVERT: C 447 GLU cc_start: 0.5863 (mm-30) cc_final: 0.5494 (pt0) REVERT: D 150 ASP cc_start: 0.8304 (m-30) cc_final: 0.7998 (m-30) REVERT: D 338 GLU cc_start: 0.6700 (mm-30) cc_final: 0.5756 (mm-30) REVERT: D 350 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8233 (tttt) REVERT: E 14 ASN cc_start: 0.8228 (p0) cc_final: 0.7774 (p0) REVERT: E 70 GLU cc_start: 0.7942 (tt0) cc_final: 0.7295 (mt-10) REVERT: E 139 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7370 (tm-30) REVERT: E 153 LYS cc_start: 0.7823 (tttt) cc_final: 0.7365 (mptp) REVERT: E 156 ASN cc_start: 0.7985 (t0) cc_final: 0.7407 (m-40) REVERT: E 166 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8109 (mp) REVERT: E 224 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7438 (tt0) REVERT: E 368 LYS cc_start: 0.7586 (mmtp) cc_final: 0.6279 (pttm) REVERT: E 373 ILE cc_start: 0.7846 (mt) cc_final: 0.7633 (mt) REVERT: E 447 GLU cc_start: 0.5416 (mm-30) cc_final: 0.5133 (pt0) REVERT: F 166 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8158 (mp) REVERT: F 332 MET cc_start: 0.7204 (mmt) cc_final: 0.6614 (mmt) REVERT: F 338 GLU cc_start: 0.6171 (mm-30) cc_final: 0.5291 (mm-30) REVERT: G 139 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: G 150 ASP cc_start: 0.8268 (m-30) cc_final: 0.7962 (m-30) REVERT: G 218 MET cc_start: 0.8315 (ttm) cc_final: 0.8032 (ttm) REVERT: G 338 GLU cc_start: 0.6663 (mm-30) cc_final: 0.5720 (mm-30) REVERT: G 347 LEU cc_start: 0.7675 (tp) cc_final: 0.7425 (mt) REVERT: G 350 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8152 (tttp) REVERT: H 14 ASN cc_start: 0.8193 (p0) cc_final: 0.7760 (p0) REVERT: H 137 MET cc_start: 0.9124 (ttt) cc_final: 0.8867 (ttt) REVERT: H 139 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: H 153 LYS cc_start: 0.7820 (tttt) cc_final: 0.7370 (mptp) REVERT: H 156 ASN cc_start: 0.8003 (t0) cc_final: 0.7418 (m-40) REVERT: H 338 GLU cc_start: 0.6202 (mm-30) cc_final: 0.5353 (mm-30) REVERT: H 368 LYS cc_start: 0.7538 (mmtp) cc_final: 0.6289 (pttm) REVERT: I 88 GLN cc_start: 0.8196 (mt0) cc_final: 0.7980 (mt0) REVERT: I 139 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: I 156 ASN cc_start: 0.7769 (t0) cc_final: 0.7245 (m-40) REVERT: I 256 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6650 (mp0) REVERT: I 332 MET cc_start: 0.7419 (mmt) cc_final: 0.7065 (mmt) REVERT: I 347 LEU cc_start: 0.7776 (tp) cc_final: 0.7441 (mt) REVERT: I 375 GLN cc_start: 0.7282 (mt0) cc_final: 0.6954 (mt0) REVERT: J 88 GLN cc_start: 0.8231 (mt0) cc_final: 0.8017 (mt0) REVERT: J 156 ASN cc_start: 0.7705 (t0) cc_final: 0.7142 (m110) REVERT: J 224 GLU cc_start: 0.7597 (tt0) cc_final: 0.7346 (tt0) REVERT: J 243 MET cc_start: 0.9149 (ttp) cc_final: 0.8868 (ttp) REVERT: J 256 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6587 (mp0) REVERT: J 332 MET cc_start: 0.7402 (mmt) cc_final: 0.6654 (mmt) REVERT: J 347 LEU cc_start: 0.7873 (tp) cc_final: 0.7551 (mt) REVERT: J 375 GLN cc_start: 0.7277 (mt0) cc_final: 0.6921 (mt0) REVERT: J 424 MET cc_start: 0.7944 (mtt) cc_final: 0.7644 (mtm) REVERT: J 447 GLU cc_start: 0.6051 (mm-30) cc_final: 0.5362 (pt0) outliers start: 101 outliers final: 43 residues processed: 656 average time/residue: 0.7136 time to fit residues: 560.2004 Evaluate side-chains 605 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 549 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 400 SER Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 350 LYS Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 400 SER Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 400 SER Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 400 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 343 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 366 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 354 HIS B 107 GLN B 354 HIS C 107 GLN C 354 HIS C 417 ASN D 107 GLN D 195 ASN D 345 ASN D 354 HIS D 429 HIS E 16 HIS E 107 GLN F 107 GLN F 345 ASN F 417 ASN F 429 HIS G 107 GLN G 345 ASN G 354 HIS G 429 HIS H 16 HIS ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 354 HIS J 68 ASN J 107 GLN J 354 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.170380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.132425 restraints weight = 28574.065| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.10 r_work: 0.3291 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 37670 Z= 0.279 Angle : 0.789 11.070 51050 Z= 0.430 Chirality : 0.051 0.218 5520 Planarity : 0.006 0.046 6610 Dihedral : 10.525 173.503 5137 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.38 % Allowed : 14.65 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.20 (0.12), residues: 4630 helix: 0.93 (0.11), residues: 2020 sheet: -0.52 (0.20), residues: 600 loop : -0.38 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 102 TYR 0.030 0.004 TYR G 20 PHE 0.031 0.003 PHE I 411 TRP 0.020 0.003 TRP H 271 HIS 0.015 0.003 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00591 (37670) covalent geometry : angle 0.78938 (51050) hydrogen bonds : bond 0.05607 ( 1593) hydrogen bonds : angle 5.54566 ( 4590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 565 time to evaluate : 1.610 Fit side-chains REVERT: A 139 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: A 218 MET cc_start: 0.8257 (ttm) cc_final: 0.7515 (ttm) REVERT: A 338 GLU cc_start: 0.6842 (mm-30) cc_final: 0.5773 (mm-30) REVERT: A 347 LEU cc_start: 0.7693 (tp) cc_final: 0.7481 (mt) REVERT: A 447 GLU cc_start: 0.5903 (mm-30) cc_final: 0.5311 (pt0) REVERT: B 139 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: B 151 MET cc_start: 0.8532 (ttm) cc_final: 0.8076 (ttm) REVERT: B 187 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7976 (t) REVERT: B 218 MET cc_start: 0.8256 (ttm) cc_final: 0.7545 (ttm) REVERT: B 256 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: B 337 GLU cc_start: 0.6468 (mp0) cc_final: 0.6222 (mp0) REVERT: B 338 GLU cc_start: 0.6745 (mm-30) cc_final: 0.5660 (mm-30) REVERT: B 347 LEU cc_start: 0.7704 (tp) cc_final: 0.7494 (mt) REVERT: B 447 GLU cc_start: 0.5861 (mm-30) cc_final: 0.5279 (pt0) REVERT: C 166 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8210 (mp) REVERT: C 338 GLU cc_start: 0.6446 (mm-30) cc_final: 0.5551 (mm-30) REVERT: C 447 GLU cc_start: 0.5862 (mm-30) cc_final: 0.5489 (pt0) REVERT: D 150 ASP cc_start: 0.8348 (m-30) cc_final: 0.8073 (m-30) REVERT: D 338 GLU cc_start: 0.6753 (mm-30) cc_final: 0.5815 (mm-30) REVERT: D 347 LEU cc_start: 0.7787 (tp) cc_final: 0.7560 (mt) REVERT: D 350 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8193 (tttp) REVERT: D 357 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6883 (tm-30) REVERT: D 359 GLU cc_start: 0.6752 (mp0) cc_final: 0.6407 (mp0) REVERT: E 11 LYS cc_start: 0.8191 (mttp) cc_final: 0.7966 (mmtp) REVERT: E 70 GLU cc_start: 0.7966 (tt0) cc_final: 0.7329 (mt-10) REVERT: E 139 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: E 153 LYS cc_start: 0.7949 (tttt) cc_final: 0.7454 (mptp) REVERT: E 156 ASN cc_start: 0.7846 (t0) cc_final: 0.7226 (m-40) REVERT: E 166 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8220 (mp) REVERT: E 338 GLU cc_start: 0.6293 (mm-30) cc_final: 0.5459 (mm-30) REVERT: E 347 LEU cc_start: 0.7904 (tp) cc_final: 0.7689 (mt) REVERT: E 365 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6022 (tm-30) REVERT: E 373 ILE cc_start: 0.7871 (mt) cc_final: 0.7635 (mt) REVERT: E 447 GLU cc_start: 0.5494 (mm-30) cc_final: 0.5206 (pt0) REVERT: F 166 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8210 (mp) REVERT: F 332 MET cc_start: 0.7317 (mmt) cc_final: 0.6852 (mmt) REVERT: F 338 GLU cc_start: 0.6342 (mm-30) cc_final: 0.5449 (mm-30) REVERT: F 365 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6286 (tm-30) REVERT: G 139 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: G 150 ASP cc_start: 0.8271 (m-30) cc_final: 0.8001 (m-30) REVERT: G 338 GLU cc_start: 0.6733 (mm-30) cc_final: 0.5809 (mm-30) REVERT: G 347 LEU cc_start: 0.7759 (tp) cc_final: 0.7519 (mt) REVERT: H 14 ASN cc_start: 0.8279 (p0) cc_final: 0.7853 (p0) REVERT: H 139 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: H 153 LYS cc_start: 0.7898 (tttt) cc_final: 0.7427 (mptp) REVERT: H 156 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7423 (m-40) REVERT: H 166 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8180 (mp) REVERT: H 338 GLU cc_start: 0.6291 (mm-30) cc_final: 0.5450 (mm-30) REVERT: I 139 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: I 156 ASN cc_start: 0.7822 (t0) cc_final: 0.7251 (m110) REVERT: I 240 PHE cc_start: 0.8423 (m-80) cc_final: 0.8084 (m-80) REVERT: I 256 GLU cc_start: 0.7546 (mt-10) cc_final: 0.6718 (mp0) REVERT: I 332 MET cc_start: 0.7538 (mmt) cc_final: 0.7117 (mmt) REVERT: I 347 LEU cc_start: 0.7890 (tp) cc_final: 0.7574 (mt) REVERT: J 77 MET cc_start: 0.8753 (mmp) cc_final: 0.8266 (mmp) REVERT: J 139 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: J 156 ASN cc_start: 0.7746 (t0) cc_final: 0.7163 (m110) REVERT: J 240 PHE cc_start: 0.8420 (m-80) cc_final: 0.8068 (m-80) REVERT: J 256 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6670 (mp0) REVERT: J 332 MET cc_start: 0.7500 (mmt) cc_final: 0.7217 (mmt) REVERT: J 347 LEU cc_start: 0.7914 (tp) cc_final: 0.7607 (mt) REVERT: J 424 MET cc_start: 0.8137 (mtt) cc_final: 0.7811 (mtm) REVERT: J 447 GLU cc_start: 0.5950 (mm-30) cc_final: 0.5268 (pt0) outliers start: 91 outliers final: 49 residues processed: 628 average time/residue: 0.8178 time to fit residues: 612.3058 Evaluate side-chains 618 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 551 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 365 GLU Chi-restraints excluded: chain E residue 400 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 245 GLU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 156 ASN Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 400 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 400 SER Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 400 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 89 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 427 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 343 optimal weight: 0.6980 chunk 302 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 337 optimal weight: 6.9990 chunk 454 optimal weight: 7.9990 chunk 279 optimal weight: 8.9990 chunk 451 optimal weight: 0.1980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 GLN ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN B 354 HIS C 107 GLN C 156 ASN D 107 GLN D 195 ASN D 333 GLN D 345 ASN D 354 HIS E 16 HIS E 107 GLN E 333 GLN F 107 GLN F 156 ASN G 107 GLN G 345 ASN G 354 HIS H 16 HIS H 107 GLN I 354 HIS J 68 ASN J 107 GLN J 354 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.173230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.136019 restraints weight = 28985.581| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.04 r_work: 0.3352 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37670 Z= 0.150 Angle : 0.632 8.621 51050 Z= 0.342 Chirality : 0.044 0.174 5520 Planarity : 0.004 0.043 6610 Dihedral : 9.837 171.235 5137 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.30 % Allowed : 15.17 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.67 % 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: 0.57 (0.12), residues: 4630 helix: 1.36 (0.11), residues: 2020 sheet: -0.53 (0.20), residues: 600 loop : -0.26 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 246 TYR 0.016 0.002 TYR G 20 PHE 0.030 0.002 PHE A 240 TRP 0.018 0.002 TRP E 97 HIS 0.006 0.002 HIS H 16 Details of bonding type rmsd covalent geometry : bond 0.00310 (37670) covalent geometry : angle 0.63210 (51050) hydrogen bonds : bond 0.04342 ( 1593) hydrogen bonds : angle 5.18649 ( 4590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 563 time to evaluate : 1.476 Fit side-chains REVERT: A 139 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: A 218 MET cc_start: 0.8271 (ttm) cc_final: 0.7589 (ttm) REVERT: A 337 GLU cc_start: 0.6375 (mp0) cc_final: 0.6149 (mp0) REVERT: A 447 GLU cc_start: 0.5852 (mm-30) cc_final: 0.5347 (pt0) REVERT: B 139 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: B 151 MET cc_start: 0.8565 (ttm) cc_final: 0.8102 (ttm) REVERT: B 218 MET cc_start: 0.8277 (ttm) cc_final: 0.7575 (ttm) REVERT: B 256 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6569 (mp0) REVERT: B 337 GLU cc_start: 0.6242 (mp0) cc_final: 0.5985 (mp0) REVERT: B 338 GLU cc_start: 0.6767 (mm-30) cc_final: 0.5714 (mm-30) REVERT: B 447 GLU cc_start: 0.5815 (mm-30) cc_final: 0.5332 (pt0) REVERT: C 86 LEU cc_start: 0.8716 (mt) cc_final: 0.8461 (mt) REVERT: C 156 ASN cc_start: 0.7468 (OUTLIER) cc_final: 0.7156 (m-40) REVERT: C 166 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8091 (mp) REVERT: C 338 GLU cc_start: 0.6308 (mm-30) cc_final: 0.5473 (mm-30) REVERT: C 447 GLU cc_start: 0.5881 (mm-30) cc_final: 0.5540 (pt0) REVERT: D 77 MET cc_start: 0.8689 (mmp) cc_final: 0.8336 (mmm) REVERT: D 150 ASP cc_start: 0.8276 (m-30) cc_final: 0.7959 (m-30) REVERT: D 338 GLU cc_start: 0.6706 (mm-30) cc_final: 0.5766 (mm-30) REVERT: D 350 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8251 (tttt) REVERT: E 11 LYS cc_start: 0.8215 (mttp) cc_final: 0.7990 (mmtp) REVERT: E 14 ASN cc_start: 0.8222 (p0) cc_final: 0.7759 (p0) REVERT: E 70 GLU cc_start: 0.7953 (tt0) cc_final: 0.7314 (mt-10) REVERT: E 139 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: E 153 LYS cc_start: 0.7844 (tttt) cc_final: 0.7398 (mptp) REVERT: E 156 ASN cc_start: 0.7999 (t0) cc_final: 0.7422 (m-40) REVERT: E 166 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8091 (mp) REVERT: E 224 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7399 (tt0) REVERT: E 347 LEU cc_start: 0.7875 (tp) cc_final: 0.7671 (mt) REVERT: E 368 LYS cc_start: 0.7604 (mmtp) cc_final: 0.6308 (pttm) REVERT: E 373 ILE cc_start: 0.7856 (mt) cc_final: 0.7638 (mt) REVERT: E 447 GLU cc_start: 0.5403 (mm-30) cc_final: 0.5155 (pt0) REVERT: F 156 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.7163 (m-40) REVERT: F 166 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8121 (mp) REVERT: F 338 GLU cc_start: 0.6205 (mm-30) cc_final: 0.5342 (mm-30) REVERT: G 77 MET cc_start: 0.8646 (mmp) cc_final: 0.8309 (mmm) REVERT: G 139 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: G 150 ASP cc_start: 0.8244 (m-30) cc_final: 0.7973 (m-30) REVERT: G 338 GLU cc_start: 0.6697 (mm-30) cc_final: 0.5770 (mm-30) REVERT: G 347 LEU cc_start: 0.7785 (tp) cc_final: 0.7572 (mt) REVERT: H 14 ASN cc_start: 0.8207 (p0) cc_final: 0.7755 (p0) REVERT: H 139 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7328 (tm-30) REVERT: H 153 LYS cc_start: 0.7815 (tttt) cc_final: 0.7368 (mptp) REVERT: H 156 ASN cc_start: 0.8017 (t0) cc_final: 0.7434 (m-40) REVERT: H 368 LYS cc_start: 0.7591 (mmtp) cc_final: 0.6358 (pttm) REVERT: I 88 GLN cc_start: 0.8234 (mt0) cc_final: 0.8010 (mt0) REVERT: I 139 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7798 (tm-30) REVERT: I 156 ASN cc_start: 0.7769 (t0) cc_final: 0.7256 (m-40) REVERT: I 256 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6677 (mp0) REVERT: I 332 MET cc_start: 0.7472 (mmt) cc_final: 0.7103 (mmt) REVERT: I 338 GLU cc_start: 0.6641 (mm-30) cc_final: 0.5584 (mm-30) REVERT: I 347 LEU cc_start: 0.7810 (tp) cc_final: 0.7494 (mt) REVERT: J 88 GLN cc_start: 0.8207 (mt0) cc_final: 0.8004 (mt0) REVERT: J 156 ASN cc_start: 0.7699 (t0) cc_final: 0.7146 (m110) REVERT: J 187 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.7766 (t) REVERT: J 256 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6621 (mp0) REVERT: J 332 MET cc_start: 0.7278 (mmt) cc_final: 0.6855 (mmt) REVERT: J 347 LEU cc_start: 0.7918 (tp) cc_final: 0.7605 (mt) REVERT: J 424 MET cc_start: 0.7868 (mtt) cc_final: 0.7632 (mtm) REVERT: J 447 GLU cc_start: 0.5945 (mm-30) cc_final: 0.5381 (pt0) outliers start: 88 outliers final: 40 residues processed: 627 average time/residue: 0.8114 time to fit residues: 605.8060 Evaluate side-chains 599 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 545 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 400 SER Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 156 ASN Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 245 GLU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 400 SER Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 400 SER Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 400 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 381 optimal weight: 2.9990 chunk 269 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 439 optimal weight: 6.9990 chunk 356 optimal weight: 0.7980 chunk 360 optimal weight: 0.9990 chunk 322 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 406 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS A 107 GLN A 354 HIS ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN B 354 HIS C 107 GLN C 345 ASN D 107 GLN D 195 ASN D 333 GLN D 345 ASN D 354 HIS E 16 HIS E 107 GLN F 107 GLN F 345 ASN G 107 GLN G 345 ASN G 354 HIS H 16 HIS H 107 GLN H 345 ASN I 16 HIS I 354 HIS J 107 GLN J 354 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.175237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.138104 restraints weight = 28966.458| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.05 r_work: 0.3378 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37670 Z= 0.131 Angle : 0.604 7.712 51050 Z= 0.325 Chirality : 0.043 0.172 5520 Planarity : 0.004 0.041 6610 Dihedral : 9.468 170.429 5131 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.06 % Allowed : 15.80 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.67 % 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 (0.12), residues: 4630 helix: 1.52 (0.11), residues: 2030 sheet: -0.57 (0.21), residues: 550 loop : -0.16 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 246 TYR 0.014 0.002 TYR G 20 PHE 0.031 0.002 PHE A 240 TRP 0.017 0.002 TRP E 97 HIS 0.006 0.002 HIS H 16 Details of bonding type rmsd covalent geometry : bond 0.00269 (37670) covalent geometry : angle 0.60431 (51050) hydrogen bonds : bond 0.04014 ( 1593) hydrogen bonds : angle 5.02987 ( 4590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 563 time to evaluate : 1.127 Fit side-chains REVERT: A 139 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: A 218 MET cc_start: 0.8258 (ttm) cc_final: 0.7550 (ttm) REVERT: A 337 GLU cc_start: 0.6290 (mp0) cc_final: 0.6028 (mp0) REVERT: A 338 GLU cc_start: 0.6727 (mm-30) cc_final: 0.5667 (mm-30) REVERT: A 447 GLU cc_start: 0.5827 (mm-30) cc_final: 0.5355 (pt0) REVERT: B 139 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: B 151 MET cc_start: 0.8568 (ttm) cc_final: 0.8114 (ttm) REVERT: B 218 MET cc_start: 0.8260 (ttm) cc_final: 0.7570 (ttm) REVERT: B 337 GLU cc_start: 0.6150 (mp0) cc_final: 0.5894 (mp0) REVERT: B 338 GLU cc_start: 0.6719 (mm-30) cc_final: 0.5648 (mm-30) REVERT: B 447 GLU cc_start: 0.5744 (mm-30) cc_final: 0.5267 (pt0) REVERT: C 86 LEU cc_start: 0.8654 (mt) cc_final: 0.8412 (mt) REVERT: C 156 ASN cc_start: 0.7581 (t0) cc_final: 0.7182 (m-40) REVERT: C 166 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7955 (mp) REVERT: C 218 MET cc_start: 0.8185 (ttm) cc_final: 0.7909 (ttm) REVERT: C 338 GLU cc_start: 0.6584 (mm-30) cc_final: 0.5745 (mm-30) REVERT: C 447 GLU cc_start: 0.5865 (mm-30) cc_final: 0.5545 (pt0) REVERT: D 77 MET cc_start: 0.8678 (mmp) cc_final: 0.8286 (mmm) REVERT: D 150 ASP cc_start: 0.8249 (m-30) cc_final: 0.7937 (m-30) REVERT: D 338 GLU cc_start: 0.6663 (mm-30) cc_final: 0.5703 (mm-30) REVERT: D 466 GLU cc_start: 0.5656 (tp30) cc_final: 0.5349 (tt0) REVERT: E 11 LYS cc_start: 0.8276 (mttp) cc_final: 0.8068 (mmtp) REVERT: E 14 ASN cc_start: 0.8137 (p0) cc_final: 0.7665 (p0) REVERT: E 70 GLU cc_start: 0.7901 (tt0) cc_final: 0.7361 (mt-10) REVERT: E 139 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: E 153 LYS cc_start: 0.7828 (tttt) cc_final: 0.7388 (mptp) REVERT: E 156 ASN cc_start: 0.7975 (t0) cc_final: 0.7412 (m-40) REVERT: E 166 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7926 (mp) REVERT: E 224 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7438 (tt0) REVERT: E 256 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6371 (mp0) REVERT: E 347 LEU cc_start: 0.7869 (tp) cc_final: 0.7663 (mt) REVERT: E 368 LYS cc_start: 0.7599 (mmtp) cc_final: 0.6302 (pttm) REVERT: E 373 ILE cc_start: 0.7838 (mt) cc_final: 0.7622 (mt) REVERT: E 447 GLU cc_start: 0.5490 (mm-30) cc_final: 0.5175 (pt0) REVERT: F 86 LEU cc_start: 0.8696 (mt) cc_final: 0.8438 (mt) REVERT: F 156 ASN cc_start: 0.7552 (t0) cc_final: 0.7162 (m-40) REVERT: F 166 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7820 (mt) REVERT: F 338 GLU cc_start: 0.6362 (mm-30) cc_final: 0.5506 (mm-30) REVERT: F 348 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7476 (mtt180) REVERT: F 357 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6630 (tm-30) REVERT: F 424 MET cc_start: 0.8128 (mtt) cc_final: 0.7814 (mtm) REVERT: G 77 MET cc_start: 0.8644 (mmp) cc_final: 0.8264 (mmm) REVERT: G 139 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: G 150 ASP cc_start: 0.8227 (m-30) cc_final: 0.7915 (m-30) REVERT: G 338 GLU cc_start: 0.6663 (mm-30) cc_final: 0.5732 (mm-30) REVERT: G 347 LEU cc_start: 0.7739 (tp) cc_final: 0.7530 (mt) REVERT: G 466 GLU cc_start: 0.5737 (tp30) cc_final: 0.5408 (tt0) REVERT: H 14 ASN cc_start: 0.8117 (p0) cc_final: 0.7684 (p0) REVERT: H 139 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: H 150 ASP cc_start: 0.8128 (m-30) cc_final: 0.7840 (m-30) REVERT: H 153 LYS cc_start: 0.7815 (tttt) cc_final: 0.7364 (mptp) REVERT: H 156 ASN cc_start: 0.7975 (t0) cc_final: 0.7411 (m-40) REVERT: H 256 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6423 (mp0) REVERT: H 338 GLU cc_start: 0.6153 (mm-30) cc_final: 0.5309 (mm-30) REVERT: H 368 LYS cc_start: 0.7666 (mmtp) cc_final: 0.6368 (pttm) REVERT: H 466 GLU cc_start: 0.5680 (tp30) cc_final: 0.5465 (tp30) REVERT: I 88 GLN cc_start: 0.8187 (mt0) cc_final: 0.7957 (mt0) REVERT: I 139 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: I 156 ASN cc_start: 0.7729 (t0) cc_final: 0.7225 (m-40) REVERT: I 187 VAL cc_start: 0.8211 (OUTLIER) cc_final: 0.7855 (t) REVERT: I 256 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6671 (mp0) REVERT: I 332 MET cc_start: 0.7473 (mmt) cc_final: 0.6821 (mmt) REVERT: I 338 GLU cc_start: 0.6504 (mm-30) cc_final: 0.5427 (mm-30) REVERT: I 347 LEU cc_start: 0.7765 (tp) cc_final: 0.7456 (mt) REVERT: J 88 GLN cc_start: 0.8245 (mt0) cc_final: 0.8031 (mt0) REVERT: J 156 ASN cc_start: 0.7657 (t0) cc_final: 0.7117 (m110) REVERT: J 187 VAL cc_start: 0.8148 (p) cc_final: 0.7803 (t) REVERT: J 256 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6573 (mp0) REVERT: J 332 MET cc_start: 0.7187 (mmt) cc_final: 0.6841 (mmt) REVERT: J 338 GLU cc_start: 0.6530 (mm-30) cc_final: 0.5487 (mm-30) REVERT: J 347 LEU cc_start: 0.7822 (tp) cc_final: 0.7490 (mt) REVERT: J 424 MET cc_start: 0.7816 (mtt) cc_final: 0.7577 (mtm) REVERT: J 447 GLU cc_start: 0.5937 (mm-30) cc_final: 0.5404 (pt0) outliers start: 79 outliers final: 36 residues processed: 625 average time/residue: 0.7470 time to fit residues: 556.5774 Evaluate side-chains 591 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 545 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 400 SER Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 400 SER Chi-restraints excluded: chain H residue 422 THR Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 400 SER Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 400 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 122 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 chunk 357 optimal weight: 7.9990 chunk 309 optimal weight: 8.9990 chunk 353 optimal weight: 0.9980 chunk 388 optimal weight: 0.5980 chunk 167 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN B 107 GLN B 354 HIS C 107 GLN D 16 HIS D 107 GLN D 195 ASN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 ASN D 354 HIS E 16 HIS E 107 GLN E 345 ASN ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN G 345 ASN G 354 HIS H 16 HIS H 107 GLN I 16 HIS ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 354 HIS J 107 GLN J 354 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.173069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.136123 restraints weight = 28649.063| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.09 r_work: 0.3336 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37670 Z= 0.178 Angle : 0.668 8.755 51050 Z= 0.360 Chirality : 0.046 0.181 5520 Planarity : 0.004 0.041 6610 Dihedral : 9.621 172.492 5126 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.96 % Allowed : 16.16 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.67 % 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: 0.64 (0.12), residues: 4630 helix: 1.41 (0.11), residues: 2030 sheet: -0.56 (0.20), residues: 600 loop : -0.18 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 279 TYR 0.020 0.003 TYR G 20 PHE 0.034 0.002 PHE A 240 TRP 0.016 0.002 TRP J 97 HIS 0.009 0.002 HIS H 16 Details of bonding type rmsd covalent geometry : bond 0.00374 (37670) covalent geometry : angle 0.66753 (51050) hydrogen bonds : bond 0.04598 ( 1593) hydrogen bonds : angle 5.16170 ( 4590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 559 time to evaluate : 1.281 Fit side-chains REVERT: A 139 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: A 218 MET cc_start: 0.8267 (ttm) cc_final: 0.7532 (ttm) REVERT: A 337 GLU cc_start: 0.6341 (mp0) cc_final: 0.6091 (mp0) REVERT: A 447 GLU cc_start: 0.5793 (mm-30) cc_final: 0.5280 (pt0) REVERT: B 139 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: B 151 MET cc_start: 0.8576 (ttm) cc_final: 0.8058 (ttm) REVERT: B 218 MET cc_start: 0.8282 (ttm) cc_final: 0.7563 (ttm) REVERT: B 338 GLU cc_start: 0.6853 (mm-30) cc_final: 0.5707 (mm-30) REVERT: B 347 LEU cc_start: 0.7635 (tp) cc_final: 0.7426 (mt) REVERT: B 447 GLU cc_start: 0.5752 (mm-30) cc_final: 0.5243 (pt0) REVERT: C 86 LEU cc_start: 0.8691 (mt) cc_final: 0.8452 (mt) REVERT: C 156 ASN cc_start: 0.7641 (t0) cc_final: 0.7205 (m-40) REVERT: C 166 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8050 (mp) REVERT: C 218 MET cc_start: 0.8311 (ttm) cc_final: 0.8040 (ttm) REVERT: C 338 GLU cc_start: 0.6664 (mm-30) cc_final: 0.5816 (mm-30) REVERT: C 447 GLU cc_start: 0.5862 (mm-30) cc_final: 0.5522 (pt0) REVERT: D 77 MET cc_start: 0.8701 (mmp) cc_final: 0.8352 (mmm) REVERT: D 150 ASP cc_start: 0.8304 (m-30) cc_final: 0.8032 (m-30) REVERT: D 338 GLU cc_start: 0.6692 (mm-30) cc_final: 0.5729 (mm-30) REVERT: D 347 LEU cc_start: 0.7756 (tp) cc_final: 0.7536 (mt) REVERT: E 11 LYS cc_start: 0.8276 (mttp) cc_final: 0.8068 (mmtp) REVERT: E 14 ASN cc_start: 0.8222 (p0) cc_final: 0.7756 (p0) REVERT: E 70 GLU cc_start: 0.7919 (tt0) cc_final: 0.7280 (mt-10) REVERT: E 139 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7433 (tm-30) REVERT: E 153 LYS cc_start: 0.7813 (tttt) cc_final: 0.7367 (mptp) REVERT: E 156 ASN cc_start: 0.7990 (t0) cc_final: 0.7416 (m-40) REVERT: E 166 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8084 (mp) REVERT: E 224 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7436 (tt0) REVERT: E 256 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6306 (mp0) REVERT: E 338 GLU cc_start: 0.6177 (mm-30) cc_final: 0.5342 (mm-30) REVERT: E 373 ILE cc_start: 0.7846 (mt) cc_final: 0.7625 (mt) REVERT: E 447 GLU cc_start: 0.5521 (mm-30) cc_final: 0.5172 (pt0) REVERT: F 86 LEU cc_start: 0.8734 (mt) cc_final: 0.8499 (mt) REVERT: F 156 ASN cc_start: 0.7621 (t0) cc_final: 0.7201 (m-40) REVERT: F 166 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8095 (mp) REVERT: F 338 GLU cc_start: 0.6530 (mm-30) cc_final: 0.5671 (mm-30) REVERT: F 357 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6782 (tm-30) REVERT: F 424 MET cc_start: 0.8233 (mtt) cc_final: 0.7865 (mtm) REVERT: G 77 MET cc_start: 0.8665 (mmp) cc_final: 0.8391 (mmm) REVERT: G 139 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: G 150 ASP cc_start: 0.8242 (m-30) cc_final: 0.7970 (m-30) REVERT: G 338 GLU cc_start: 0.6695 (mm-30) cc_final: 0.5741 (mm-30) REVERT: G 347 LEU cc_start: 0.7830 (tp) cc_final: 0.7598 (mt) REVERT: H 14 ASN cc_start: 0.8203 (p0) cc_final: 0.7761 (p0) REVERT: H 139 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: H 153 LYS cc_start: 0.7814 (tttt) cc_final: 0.7348 (mptp) REVERT: H 156 ASN cc_start: 0.8012 (t0) cc_final: 0.7428 (m-40) REVERT: H 256 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6450 (mp0) REVERT: H 338 GLU cc_start: 0.6157 (mm-30) cc_final: 0.5319 (mm-30) REVERT: H 368 LYS cc_start: 0.7581 (mmtp) cc_final: 0.6341 (pttm) REVERT: I 88 GLN cc_start: 0.8206 (mt0) cc_final: 0.7973 (mt0) REVERT: I 139 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: I 156 ASN cc_start: 0.7766 (t0) cc_final: 0.7225 (m110) REVERT: I 187 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7820 (t) REVERT: I 240 PHE cc_start: 0.8287 (m-80) cc_final: 0.8064 (m-80) REVERT: I 256 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6704 (mp0) REVERT: I 332 MET cc_start: 0.7452 (mmt) cc_final: 0.7086 (mmt) REVERT: I 338 GLU cc_start: 0.6523 (mm-30) cc_final: 0.5411 (mm-30) REVERT: I 347 LEU cc_start: 0.7818 (tp) cc_final: 0.7494 (mt) REVERT: J 88 GLN cc_start: 0.8223 (mt0) cc_final: 0.7995 (mt0) REVERT: J 156 ASN cc_start: 0.7685 (t0) cc_final: 0.7141 (m-40) REVERT: J 187 VAL cc_start: 0.8129 (p) cc_final: 0.7759 (t) REVERT: J 240 PHE cc_start: 0.8284 (m-80) cc_final: 0.8055 (m-80) REVERT: J 256 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6566 (mp0) REVERT: J 332 MET cc_start: 0.7321 (mmt) cc_final: 0.6607 (mmt) REVERT: J 338 GLU cc_start: 0.6674 (mm-30) cc_final: 0.5562 (mm-30) REVERT: J 347 LEU cc_start: 0.7884 (tp) cc_final: 0.7549 (mt) REVERT: J 424 MET cc_start: 0.7904 (mtt) cc_final: 0.7616 (mtm) REVERT: J 447 GLU cc_start: 0.5938 (mm-30) cc_final: 0.5379 (pt0) outliers start: 75 outliers final: 42 residues processed: 615 average time/residue: 0.6926 time to fit residues: 507.9333 Evaluate side-chains 597 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 545 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 400 SER Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 400 SER Chi-restraints excluded: chain H residue 422 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 400 SER Chi-restraints excluded: chain J residue 400 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 269 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 416 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 301 optimal weight: 6.9990 chunk 367 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 343 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 GLN A 354 HIS ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN B 354 HIS C 107 GLN C 345 ASN D 16 HIS D 107 GLN D 195 ASN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS E 16 HIS E 107 GLN F 107 GLN F 345 ASN G 107 GLN G 195 ASN G 354 HIS H 16 HIS ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN I 16 HIS ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 354 HIS J 107 GLN J 354 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.172109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.134870 restraints weight = 28789.571| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.17 r_work: 0.3324 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 37670 Z= 0.205 Angle : 0.710 9.466 51050 Z= 0.384 Chirality : 0.047 0.181 5520 Planarity : 0.005 0.041 6610 Dihedral : 9.789 172.918 5126 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.88 % Allowed : 16.29 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.67 % 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: 0.51 (0.12), residues: 4630 helix: 1.26 (0.11), residues: 2030 sheet: -0.61 (0.20), residues: 600 loop : -0.20 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 160 TYR 0.023 0.003 TYR G 20 PHE 0.036 0.003 PHE A 240 TRP 0.016 0.002 TRP H 97 HIS 0.011 0.002 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00431 (37670) covalent geometry : angle 0.70964 (51050) hydrogen bonds : bond 0.04926 ( 1593) hydrogen bonds : angle 5.28575 ( 4590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 557 time to evaluate : 1.029 Fit side-chains REVERT: A 139 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: A 218 MET cc_start: 0.8263 (ttm) cc_final: 0.7511 (ttm) REVERT: A 337 GLU cc_start: 0.6332 (mp0) cc_final: 0.6071 (mp0) REVERT: A 338 GLU cc_start: 0.6765 (mm-30) cc_final: 0.5687 (mm-30) REVERT: A 347 LEU cc_start: 0.7641 (tp) cc_final: 0.7431 (mt) REVERT: A 447 GLU cc_start: 0.5870 (mm-30) cc_final: 0.5365 (pt0) REVERT: B 139 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: B 151 MET cc_start: 0.8591 (ttm) cc_final: 0.8185 (ttm) REVERT: B 218 MET cc_start: 0.8281 (ttm) cc_final: 0.7542 (ttm) REVERT: B 337 GLU cc_start: 0.6263 (mp0) cc_final: 0.6018 (mp0) REVERT: B 338 GLU cc_start: 0.6748 (mm-30) cc_final: 0.5582 (mm-30) REVERT: B 347 LEU cc_start: 0.7635 (tp) cc_final: 0.7431 (mt) REVERT: B 447 GLU cc_start: 0.5832 (mm-30) cc_final: 0.5323 (pt0) REVERT: C 86 LEU cc_start: 0.8744 (mt) cc_final: 0.8535 (mt) REVERT: C 156 ASN cc_start: 0.7667 (t0) cc_final: 0.7191 (m-40) REVERT: C 166 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8151 (mp) REVERT: C 338 GLU cc_start: 0.6391 (mm-30) cc_final: 0.5569 (mm-30) REVERT: C 447 GLU cc_start: 0.5917 (mm-30) cc_final: 0.5579 (pt0) REVERT: D 150 ASP cc_start: 0.8306 (m-30) cc_final: 0.8040 (m-30) REVERT: D 338 GLU cc_start: 0.6671 (mm-30) cc_final: 0.5704 (mm-30) REVERT: D 347 LEU cc_start: 0.7759 (tp) cc_final: 0.7535 (mt) REVERT: E 11 LYS cc_start: 0.8205 (mttp) cc_final: 0.7991 (mmtp) REVERT: E 14 ASN cc_start: 0.8226 (p0) cc_final: 0.7763 (p0) REVERT: E 70 GLU cc_start: 0.7920 (tt0) cc_final: 0.7257 (mt-10) REVERT: E 139 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: E 153 LYS cc_start: 0.7845 (tttt) cc_final: 0.7359 (mptp) REVERT: E 156 ASN cc_start: 0.8016 (t0) cc_final: 0.7428 (m-40) REVERT: E 166 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8109 (mp) REVERT: E 224 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7455 (tt0) REVERT: E 256 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6277 (mp0) REVERT: E 338 GLU cc_start: 0.6187 (mm-30) cc_final: 0.5350 (mm-30) REVERT: E 373 ILE cc_start: 0.7838 (mt) cc_final: 0.7622 (mt) REVERT: E 447 GLU cc_start: 0.5559 (mm-30) cc_final: 0.5209 (pt0) REVERT: F 156 ASN cc_start: 0.7694 (t0) cc_final: 0.7224 (m-40) REVERT: F 166 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8154 (mp) REVERT: F 338 GLU cc_start: 0.6194 (mm-30) cc_final: 0.5317 (mm-30) REVERT: F 357 GLU cc_start: 0.7316 (tm-30) cc_final: 0.7089 (tm-30) REVERT: G 139 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: G 150 ASP cc_start: 0.8245 (m-30) cc_final: 0.7981 (m-30) REVERT: G 224 GLU cc_start: 0.7460 (tt0) cc_final: 0.7094 (mt-10) REVERT: G 338 GLU cc_start: 0.6674 (mm-30) cc_final: 0.5729 (mm-30) REVERT: G 347 LEU cc_start: 0.7792 (tp) cc_final: 0.7564 (mt) REVERT: G 357 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: H 14 ASN cc_start: 0.8219 (p0) cc_final: 0.7785 (p0) REVERT: H 139 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: H 153 LYS cc_start: 0.7834 (tttt) cc_final: 0.7347 (mptp) REVERT: H 156 ASN cc_start: 0.8007 (t0) cc_final: 0.7416 (m-40) REVERT: H 256 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6459 (mp0) REVERT: H 338 GLU cc_start: 0.6159 (mm-30) cc_final: 0.5325 (mm-30) REVERT: H 347 LEU cc_start: 0.7822 (tp) cc_final: 0.7613 (mt) REVERT: I 88 GLN cc_start: 0.8205 (mt0) cc_final: 0.7977 (mt0) REVERT: I 139 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: I 156 ASN cc_start: 0.7768 (t0) cc_final: 0.7213 (m110) REVERT: I 187 VAL cc_start: 0.8168 (p) cc_final: 0.7842 (t) REVERT: I 240 PHE cc_start: 0.8338 (m-80) cc_final: 0.8068 (m-80) REVERT: I 256 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6695 (mp0) REVERT: I 332 MET cc_start: 0.7453 (mmt) cc_final: 0.7055 (mmt) REVERT: I 347 LEU cc_start: 0.7823 (tp) cc_final: 0.7501 (mt) REVERT: J 88 GLN cc_start: 0.8254 (mt0) cc_final: 0.8038 (mt0) REVERT: J 156 ASN cc_start: 0.7680 (t0) cc_final: 0.7133 (m-40) REVERT: J 187 VAL cc_start: 0.8114 (p) cc_final: 0.7793 (t) REVERT: J 240 PHE cc_start: 0.8322 (m-80) cc_final: 0.8044 (m-80) REVERT: J 256 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6622 (mp0) REVERT: J 338 GLU cc_start: 0.6646 (mm-30) cc_final: 0.5516 (mm-30) REVERT: J 347 LEU cc_start: 0.7888 (tp) cc_final: 0.7559 (mt) REVERT: J 424 MET cc_start: 0.7978 (mtt) cc_final: 0.7679 (mtm) REVERT: J 447 GLU cc_start: 0.5974 (mm-30) cc_final: 0.5411 (pt0) outliers start: 72 outliers final: 39 residues processed: 612 average time/residue: 0.7276 time to fit residues: 529.8931 Evaluate side-chains 596 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 547 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 400 SER Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 400 SER Chi-restraints excluded: chain H residue 422 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 400 SER Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 400 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 442 optimal weight: 9.9990 chunk 312 optimal weight: 0.9980 chunk 336 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 309 optimal weight: 4.9990 chunk 372 optimal weight: 0.0470 chunk 210 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 262 optimal weight: 7.9990 chunk 257 optimal weight: 0.9990 chunk 362 optimal weight: 10.0000 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS A 107 GLN B 16 HIS B 107 GLN B 354 HIS C 107 GLN C 345 ASN D 16 HIS D 107 GLN D 195 ASN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 ASN D 354 HIS E 16 HIS E 107 GLN E 345 ASN F 107 GLN G 107 GLN G 195 ASN G 345 ASN G 354 HIS H 16 HIS H 107 GLN H 345 ASN I 16 HIS I 354 HIS J 107 GLN J 354 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.175186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.138007 restraints weight = 28941.503| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.05 r_work: 0.3376 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37670 Z= 0.135 Angle : 0.619 7.968 51050 Z= 0.333 Chirality : 0.044 0.173 5520 Planarity : 0.004 0.042 6610 Dihedral : 9.395 170.491 5125 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.64 % Allowed : 16.53 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.67 % 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: 0.69 (0.12), residues: 4630 helix: 1.48 (0.11), residues: 2030 sheet: -0.68 (0.19), residues: 650 loop : -0.10 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 160 TYR 0.015 0.002 TYR G 20 PHE 0.037 0.002 PHE A 240 TRP 0.018 0.002 TRP J 97 HIS 0.007 0.002 HIS E 16 Details of bonding type rmsd covalent geometry : bond 0.00281 (37670) covalent geometry : angle 0.61928 (51050) hydrogen bonds : bond 0.04093 ( 1593) hydrogen bonds : angle 5.07072 ( 4590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9260 Ramachandran restraints generated. 4630 Oldfield, 0 Emsley, 4630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 545 time to evaluate : 1.332 Fit side-chains REVERT: A 139 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: A 218 MET cc_start: 0.8255 (ttm) cc_final: 0.7552 (ttm) REVERT: A 337 GLU cc_start: 0.6239 (mp0) cc_final: 0.5986 (mp0) REVERT: A 447 GLU cc_start: 0.5854 (mm-30) cc_final: 0.5378 (pt0) REVERT: B 139 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: B 151 MET cc_start: 0.8566 (ttm) cc_final: 0.8203 (ttm) REVERT: B 218 MET cc_start: 0.8270 (ttm) cc_final: 0.7584 (ttm) REVERT: B 337 GLU cc_start: 0.6120 (mp0) cc_final: 0.5902 (mp0) REVERT: B 338 GLU cc_start: 0.6637 (mm-30) cc_final: 0.5516 (mm-30) REVERT: B 447 GLU cc_start: 0.5769 (mm-30) cc_final: 0.5282 (pt0) REVERT: C 86 LEU cc_start: 0.8657 (mt) cc_final: 0.8424 (mt) REVERT: C 156 ASN cc_start: 0.7698 (t0) cc_final: 0.7249 (m-40) REVERT: C 166 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8018 (mp) REVERT: C 338 GLU cc_start: 0.6557 (mm-30) cc_final: 0.5707 (mm-30) REVERT: C 447 GLU cc_start: 0.5894 (mm-30) cc_final: 0.5591 (pt0) REVERT: D 77 MET cc_start: 0.8680 (mmp) cc_final: 0.8287 (mmm) REVERT: D 150 ASP cc_start: 0.8244 (m-30) cc_final: 0.7925 (m-30) REVERT: D 338 GLU cc_start: 0.6660 (mm-30) cc_final: 0.5692 (mm-30) REVERT: D 347 LEU cc_start: 0.7753 (tp) cc_final: 0.7549 (mt) REVERT: E 11 LYS cc_start: 0.8268 (mttp) cc_final: 0.8062 (mmtp) REVERT: E 14 ASN cc_start: 0.8126 (p0) cc_final: 0.7660 (p0) REVERT: E 70 GLU cc_start: 0.7900 (tt0) cc_final: 0.7277 (mt-10) REVERT: E 139 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: E 150 ASP cc_start: 0.8102 (m-30) cc_final: 0.7800 (m-30) REVERT: E 153 LYS cc_start: 0.7838 (tttt) cc_final: 0.7383 (mptp) REVERT: E 156 ASN cc_start: 0.7998 (t0) cc_final: 0.7432 (m-40) REVERT: E 166 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8054 (mp) REVERT: E 256 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6422 (mp0) REVERT: E 338 GLU cc_start: 0.6143 (mm-30) cc_final: 0.5314 (mm-30) REVERT: E 368 LYS cc_start: 0.7526 (mmtp) cc_final: 0.6252 (pttm) REVERT: E 373 ILE cc_start: 0.7830 (mt) cc_final: 0.7630 (mt) REVERT: E 447 GLU cc_start: 0.5545 (mm-30) cc_final: 0.5219 (pt0) REVERT: F 86 LEU cc_start: 0.8736 (mt) cc_final: 0.8460 (mt) REVERT: F 156 ASN cc_start: 0.7677 (t0) cc_final: 0.7235 (m-40) REVERT: F 166 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8040 (mp) REVERT: F 338 GLU cc_start: 0.6455 (mm-30) cc_final: 0.5619 (mm-30) REVERT: F 357 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6637 (tm-30) REVERT: G 77 MET cc_start: 0.8652 (mmp) cc_final: 0.8266 (mmm) REVERT: G 139 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: G 150 ASP cc_start: 0.8215 (m-30) cc_final: 0.7897 (m-30) REVERT: G 338 GLU cc_start: 0.6664 (mm-30) cc_final: 0.5730 (mm-30) REVERT: G 347 LEU cc_start: 0.7759 (tp) cc_final: 0.7546 (mt) REVERT: H 14 ASN cc_start: 0.8131 (p0) cc_final: 0.7693 (p0) REVERT: H 139 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: H 150 ASP cc_start: 0.8139 (m-30) cc_final: 0.7853 (m-30) REVERT: H 153 LYS cc_start: 0.7834 (tttt) cc_final: 0.7361 (mptp) REVERT: H 156 ASN cc_start: 0.7987 (t0) cc_final: 0.7414 (m-40) REVERT: H 256 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6505 (mp0) REVERT: H 338 GLU cc_start: 0.6127 (mm-30) cc_final: 0.5295 (mm-30) REVERT: H 368 LYS cc_start: 0.7708 (mmtp) cc_final: 0.6380 (pttm) REVERT: I 88 GLN cc_start: 0.8203 (mt0) cc_final: 0.7966 (mt0) REVERT: I 139 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: I 156 ASN cc_start: 0.7721 (t0) cc_final: 0.7211 (m-40) REVERT: I 187 VAL cc_start: 0.8041 (p) cc_final: 0.7802 (t) REVERT: I 256 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6697 (mp0) REVERT: I 332 MET cc_start: 0.7433 (mmt) cc_final: 0.6801 (mmt) REVERT: I 338 GLU cc_start: 0.6567 (mm-30) cc_final: 0.5475 (mm-30) REVERT: I 347 LEU cc_start: 0.7768 (tp) cc_final: 0.7466 (mt) REVERT: J 88 GLN cc_start: 0.8225 (mt0) cc_final: 0.7999 (mt0) REVERT: J 139 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: J 156 ASN cc_start: 0.7656 (t0) cc_final: 0.7132 (m-40) REVERT: J 256 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6561 (mp0) REVERT: J 338 GLU cc_start: 0.6635 (mm-30) cc_final: 0.5543 (mm-30) REVERT: J 347 LEU cc_start: 0.7827 (tp) cc_final: 0.7506 (mt) REVERT: J 424 MET cc_start: 0.7818 (mtt) cc_final: 0.7593 (mtm) REVERT: J 447 GLU cc_start: 0.5952 (mm-30) cc_final: 0.5419 (pt0) outliers start: 63 outliers final: 36 residues processed: 593 average time/residue: 0.7549 time to fit residues: 533.9941 Evaluate side-chains 587 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 541 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 400 SER Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 400 SER Chi-restraints excluded: chain H residue 422 THR Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 400 SER Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 400 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 165 optimal weight: 4.9990 chunk 344 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 272 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 320 optimal weight: 0.9990 chunk 403 optimal weight: 7.9990 chunk 269 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS A 107 GLN A 354 HIS B 16 HIS B 107 GLN B 354 HIS C 107 GLN D 16 HIS D 107 GLN D 195 ASN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 ASN D 354 HIS E 16 HIS E 107 GLN F 107 GLN F 345 ASN G 107 GLN G 195 ASN G 345 ASN G 354 HIS G 429 HIS H 16 HIS ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN I 16 HIS ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 354 HIS J 16 HIS J 107 GLN J 354 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.173209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135983 restraints weight = 28683.090| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.06 r_work: 0.3335 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37670 Z= 0.178 Angle : 0.679 8.698 51050 Z= 0.366 Chirality : 0.046 0.183 5520 Planarity : 0.004 0.043 6610 Dihedral : 9.562 172.946 5122 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.62 % Allowed : 16.71 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.67 % 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: 0.62 (0.12), residues: 4630 helix: 1.34 (0.11), residues: 2030 sheet: -0.60 (0.20), residues: 600 loop : -0.12 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 160 TYR 0.020 0.003 TYR G 20 PHE 0.039 0.002 PHE A 240 TRP 0.016 0.002 TRP J 97 HIS 0.009 0.002 HIS E 16 Details of bonding type rmsd covalent geometry : bond 0.00374 (37670) covalent geometry : angle 0.67948 (51050) hydrogen bonds : bond 0.04623 ( 1593) hydrogen bonds : angle 5.17830 ( 4590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17355.30 seconds wall clock time: 296 minutes 19.33 seconds (17779.33 seconds total)