Starting phenix.real_space_refine on Fri May 23 12:56:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihr_35453/05_2025/8ihr_35453.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihr_35453/05_2025/8ihr_35453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihr_35453/05_2025/8ihr_35453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihr_35453/05_2025/8ihr_35453.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihr_35453/05_2025/8ihr_35453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihr_35453/05_2025/8ihr_35453.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.065 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: 5 Type Number sf(0) Gaussians Zn 16 6.06 5 S 72 5.16 5 C 15184 2.51 5 N 4424 2.21 5 O 4528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24224 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Time building chain proxies: 14.22, per 1000 atoms: 0.59 Number of scatterers: 24224 At special positions: 0 Unit cell: (138.55, 138.55, 103.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 16 29.99 S 72 16.00 O 4528 8.00 N 4424 7.00 C 15184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 75 " distance=2.03 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: 5.46 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 85 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 251 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 271 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 83 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 85 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 271 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 251 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 83 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 85 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 251 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 271 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 83 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 85 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 271 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 251 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 83 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 85 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 251 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 271 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 83 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 85 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 251 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 271 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 83 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 85 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" ND1 HIS G 251 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 271 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 83 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 85 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" ND1 HIS H 251 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 271 " 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5680 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 28 sheets defined 43.2% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.547A pdb=" N HIS A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 230 through 245 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.607A pdb=" N GLY A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 323 removed outlier: 4.435A pdb=" N ALA A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.854A pdb=" N VAL A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.676A pdb=" N HIS A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'B' and resid 93 through 101 removed outlier: 3.655A pdb=" N GLU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE B 99 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 removed outlier: 3.551A pdb=" N HIS B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 171 through 179 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.502A pdb=" N ASP B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 293 through 304 removed outlier: 3.598A pdb=" N GLY B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 323 removed outlier: 4.420A pdb=" N ALA B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 Processing helix chain 'B' and resid 354 through 362 removed outlier: 3.933A pdb=" N VAL B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 383 removed outlier: 4.700A pdb=" N HIS B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 removed outlier: 3.545A pdb=" N ALA B 411 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 101 removed outlier: 3.653A pdb=" N GLU C 97 " --> pdb=" O GLN C 93 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASP C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 120 removed outlier: 3.547A pdb=" N HIS C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 Processing helix chain 'C' and resid 171 through 179 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 190 through 204 Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.503A pdb=" N ASP C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 293 through 304 removed outlier: 3.604A pdb=" N GLY C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 323 removed outlier: 4.420A pdb=" N ALA C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.937A pdb=" N VAL C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 383 removed outlier: 4.700A pdb=" N HIS C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN C 380 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 removed outlier: 3.589A pdb=" N ALA C 411 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 101 removed outlier: 3.655A pdb=" N GLU D 97 " --> pdb=" O GLN D 93 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE D 99 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.551A pdb=" N HIS D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 143 Processing helix chain 'D' and resid 171 through 179 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.502A pdb=" N ASP D 243 " --> pdb=" O ASP D 239 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 276 through 287 Processing helix chain 'D' and resid 293 through 304 removed outlier: 3.598A pdb=" N GLY D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 323 removed outlier: 4.419A pdb=" N ALA D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.932A pdb=" N VAL D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 383 removed outlier: 4.700A pdb=" N HIS D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 380 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 removed outlier: 3.545A pdb=" N ALA D 411 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 96 through 101 Processing helix chain 'E' and resid 102 through 120 removed outlier: 4.163A pdb=" N GLY E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 143 Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.538A pdb=" N TYR E 244 " --> pdb=" O THR E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 276 through 287 Processing helix chain 'E' and resid 293 through 304 removed outlier: 3.651A pdb=" N GLY E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 323 removed outlier: 4.531A pdb=" N ALA E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 335 removed outlier: 3.543A pdb=" N ASN E 335 " --> pdb=" O LYS E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 362 removed outlier: 3.916A pdb=" N VAL E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 383 removed outlier: 3.537A pdb=" N ALA E 374 " --> pdb=" O ALA E 370 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N HIS E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN E 380 " --> pdb=" O VAL E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 413 removed outlier: 3.589A pdb=" N ALA E 411 " --> pdb=" O ASP E 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 96 through 101 Processing helix chain 'F' and resid 102 through 120 removed outlier: 4.164A pdb=" N GLY F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 143 Processing helix chain 'F' and resid 171 through 179 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 230 through 244 removed outlier: 3.531A pdb=" N TYR F 244 " --> pdb=" O THR F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 276 through 287 Processing helix chain 'F' and resid 293 through 304 removed outlier: 3.639A pdb=" N GLY F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 323 removed outlier: 4.528A pdb=" N ALA F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 335 removed outlier: 3.502A pdb=" N ASN F 335 " --> pdb=" O LYS F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 362 removed outlier: 3.912A pdb=" N VAL F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 383 removed outlier: 3.539A pdb=" N ALA F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS F 377 " --> pdb=" O ALA F 373 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN F 380 " --> pdb=" O VAL F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 413 removed outlier: 3.583A pdb=" N ALA F 411 " --> pdb=" O ASP F 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 95 No H-bonds generated for 'chain 'G' and resid 93 through 95' Processing helix chain 'G' and resid 96 through 101 Processing helix chain 'G' and resid 102 through 120 removed outlier: 4.164A pdb=" N GLY G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 143 Processing helix chain 'G' and resid 171 through 179 Processing helix chain 'G' and resid 190 through 204 Processing helix chain 'G' and resid 230 through 244 removed outlier: 3.541A pdb=" N TYR G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 265 Processing helix chain 'G' and resid 276 through 287 Processing helix chain 'G' and resid 293 through 304 removed outlier: 3.651A pdb=" N GLY G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 323 removed outlier: 4.528A pdb=" N ALA G 323 " --> pdb=" O ALA G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 335 removed outlier: 3.520A pdb=" N ASN G 335 " --> pdb=" O LYS G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 362 removed outlier: 3.914A pdb=" N VAL G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 383 removed outlier: 3.537A pdb=" N ALA G 374 " --> pdb=" O ALA G 370 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N HIS G 377 " --> pdb=" O ALA G 373 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA G 378 " --> pdb=" O ALA G 374 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN G 380 " --> pdb=" O VAL G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 413 removed outlier: 3.588A pdb=" N ALA G 411 " --> pdb=" O ASP G 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 95 No H-bonds generated for 'chain 'H' and resid 93 through 95' Processing helix chain 'H' and resid 96 through 101 Processing helix chain 'H' and resid 102 through 120 removed outlier: 4.163A pdb=" N GLY H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 143 Processing helix chain 'H' and resid 171 through 179 Processing helix chain 'H' and resid 190 through 204 Processing helix chain 'H' and resid 230 through 244 removed outlier: 3.540A pdb=" N TYR H 244 " --> pdb=" O THR H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 265 Processing helix chain 'H' and resid 276 through 287 Processing helix chain 'H' and resid 293 through 304 removed outlier: 3.639A pdb=" N GLY H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 323 removed outlier: 4.527A pdb=" N ALA H 323 " --> pdb=" O ALA H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 335 removed outlier: 3.672A pdb=" N ASN H 335 " --> pdb=" O LYS H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 362 removed outlier: 3.917A pdb=" N VAL H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 383 removed outlier: 3.540A pdb=" N ALA H 374 " --> pdb=" O ALA H 370 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS H 377 " --> pdb=" O ALA H 373 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA H 378 " --> pdb=" O ALA H 374 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN H 380 " --> pdb=" O VAL H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 413 removed outlier: 3.590A pdb=" N ALA H 411 " --> pdb=" O ASP H 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 56 removed outlier: 5.174A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA A 47 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 13.946A pdb=" N VAL A 23 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 13.870A pdb=" N GLY A 71 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 12.414A pdb=" N VAL A 25 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N LYS A 73 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS A 27 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS A 75 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG A 29 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 398 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 418 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA A 400 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL A 418 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP A 79 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ARG A 126 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP A 81 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 212 removed outlier: 6.563A pdb=" N ILE A 209 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N HIS A 251 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE A 211 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL A 248 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLU A 270 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 250 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 56 removed outlier: 5.177A pdb=" N ILE B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA B 47 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 13.910A pdb=" N VAL B 23 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 13.891A pdb=" N GLY B 71 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 12.464A pdb=" N VAL B 25 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N LYS B 73 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N CYS B 27 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS B 75 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG B 29 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B 398 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 418 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA B 400 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 418 " --> pdb=" O TYR B 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 84 removed outlier: 6.328A pdb=" N TRP B 79 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ARG B 126 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASP B 81 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.562A pdb=" N ILE B 209 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N HIS B 251 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE B 211 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 248 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLU B 270 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA B 250 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 56 removed outlier: 5.176A pdb=" N ILE C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA C 47 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 13.914A pdb=" N VAL C 23 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 13.897A pdb=" N GLY C 71 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 12.444A pdb=" N VAL C 25 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N LYS C 73 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N CYS C 27 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N CYS C 75 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG C 29 " --> pdb=" O CYS C 75 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 398 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL C 418 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA C 400 " --> pdb=" O ARG C 416 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL C 418 " --> pdb=" O TYR C 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 79 through 84 removed outlier: 6.330A pdb=" N TRP C 79 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ARG C 126 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP C 81 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 209 through 212 removed outlier: 6.562A pdb=" N ILE C 209 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N HIS C 251 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE C 211 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL C 248 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N GLU C 270 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA C 250 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 50 through 56 removed outlier: 5.176A pdb=" N ILE D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA D 47 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 13.919A pdb=" N VAL D 23 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 13.904A pdb=" N GLY D 71 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 12.454A pdb=" N VAL D 25 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N LYS D 73 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS D 27 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS D 75 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG D 29 " --> pdb=" O CYS D 75 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D 398 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL D 418 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA D 400 " --> pdb=" O ARG D 416 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL D 418 " --> pdb=" O TYR D 425 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.335A pdb=" N TRP D 79 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ARG D 126 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP D 81 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 209 through 212 removed outlier: 6.562A pdb=" N ILE D 209 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N HIS D 251 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE D 211 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL D 248 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N GLU D 270 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA D 250 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 37 through 38 removed outlier: 3.537A pdb=" N GLN E 37 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR E 43 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL E 54 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU E 45 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 37 through 38 removed outlier: 3.537A pdb=" N GLN E 37 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 13.911A pdb=" N VAL E 23 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 14.310A pdb=" N GLY E 71 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 12.618A pdb=" N VAL E 25 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 11.106A pdb=" N LYS E 73 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS E 27 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N CYS E 75 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG E 29 " --> pdb=" O CYS E 75 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N PHE E 31 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL E 398 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL E 418 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA E 400 " --> pdb=" O ARG E 416 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL E 418 " --> pdb=" O TYR E 425 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 84 removed outlier: 6.453A pdb=" N TRP E 79 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ARG E 126 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP E 81 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 209 through 212 removed outlier: 6.629A pdb=" N ILE E 209 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N HIS E 251 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE E 211 " --> pdb=" O HIS E 251 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL E 248 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLU E 270 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA E 250 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE E 269 " --> pdb=" O VAL E 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.546A pdb=" N GLN F 37 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR F 43 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL F 54 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU F 45 " --> pdb=" O ARG F 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.546A pdb=" N GLN F 37 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 13.907A pdb=" N VAL F 23 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 14.309A pdb=" N GLY F 71 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 12.620A pdb=" N VAL F 25 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N LYS F 73 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N CYS F 27 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS F 75 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG F 29 " --> pdb=" O CYS F 75 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N PHE F 31 " --> pdb=" O PRO F 77 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL F 398 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL F 418 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA F 400 " --> pdb=" O ARG F 416 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL F 418 " --> pdb=" O TYR F 425 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 79 through 84 removed outlier: 6.454A pdb=" N TRP F 79 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ARG F 126 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP F 81 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 209 through 212 removed outlier: 6.628A pdb=" N ILE F 209 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N HIS F 251 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE F 211 " --> pdb=" O HIS F 251 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL F 248 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N GLU F 270 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA F 250 " --> pdb=" O GLU F 270 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE F 269 " --> pdb=" O VAL F 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 37 through 38 removed outlier: 3.540A pdb=" N GLN G 37 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR G 43 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL G 54 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU G 45 " --> pdb=" O ARG G 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 37 through 38 removed outlier: 3.540A pdb=" N GLN G 37 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 13.906A pdb=" N VAL G 23 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 14.310A pdb=" N GLY G 71 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 12.619A pdb=" N VAL G 25 " --> pdb=" O GLY G 71 " (cutoff:3.500A) removed outlier: 11.111A pdb=" N LYS G 73 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS G 27 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N CYS G 75 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG G 29 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N PHE G 31 " --> pdb=" O PRO G 77 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL G 398 " --> pdb=" O VAL G 418 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL G 418 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA G 400 " --> pdb=" O ARG G 416 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL G 418 " --> pdb=" O TYR G 425 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 79 through 84 removed outlier: 6.455A pdb=" N TRP G 79 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ARG G 126 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP G 81 " --> pdb=" O ARG G 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 209 through 212 removed outlier: 6.630A pdb=" N ILE G 209 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N HIS G 251 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE G 211 " --> pdb=" O HIS G 251 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL G 248 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N GLU G 270 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA G 250 " --> pdb=" O GLU G 270 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE G 269 " --> pdb=" O VAL G 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'H' and resid 37 through 38 removed outlier: 3.542A pdb=" N GLN H 37 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR H 43 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL H 54 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU H 45 " --> pdb=" O ARG H 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 37 through 38 removed outlier: 3.542A pdb=" N GLN H 37 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 13.904A pdb=" N VAL H 23 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 14.309A pdb=" N GLY H 71 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 12.610A pdb=" N VAL H 25 " --> pdb=" O GLY H 71 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N LYS H 73 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS H 27 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N CYS H 75 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG H 29 " --> pdb=" O CYS H 75 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N PHE H 31 " --> pdb=" O PRO H 77 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL H 398 " --> pdb=" O VAL H 418 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL H 418 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA H 400 " --> pdb=" O ARG H 416 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL H 418 " --> pdb=" O TYR H 425 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 79 through 84 removed outlier: 6.452A pdb=" N TRP H 79 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ARG H 126 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP H 81 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 209 through 212 removed outlier: 6.631A pdb=" N ILE H 209 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N HIS H 251 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE H 211 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL H 248 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLU H 270 " --> pdb=" O VAL H 248 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA H 250 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE H 269 " --> pdb=" O VAL H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 1001 hydrogen bonds defined for protein. 2820 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: 8.93 Time building geometry restraints manager: 6.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4626 1.32 - 1.45: 6097 1.45 - 1.57: 13853 1.57 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 24704 Sorted by residual: bond pdb=" NZ KCX E 210 " pdb=" CX KCX E 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX A 210 " pdb=" CX KCX A 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX D 210 " pdb=" CX KCX D 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX G 210 " pdb=" CX KCX G 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" NZ KCX H 210 " pdb=" CX KCX H 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 24699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 32907 2.21 - 4.43: 495 4.43 - 6.64: 59 6.64 - 8.85: 26 8.85 - 11.07: 9 Bond angle restraints: 33496 Sorted by residual: angle pdb=" N VAL C 347 " pdb=" CA VAL C 347 " pdb=" C VAL C 347 " ideal model delta sigma weight residual 111.67 101.21 10.46 9.50e-01 1.11e+00 1.21e+02 angle pdb=" N VAL A 347 " pdb=" CA VAL A 347 " pdb=" C VAL A 347 " ideal model delta sigma weight residual 111.67 101.42 10.25 9.50e-01 1.11e+00 1.16e+02 angle pdb=" N GLY C 346 " pdb=" CA GLY C 346 " pdb=" C GLY C 346 " ideal model delta sigma weight residual 113.18 102.11 11.07 2.37e+00 1.78e-01 2.18e+01 angle pdb=" C GLN C 345 " pdb=" CA GLN C 345 " pdb=" CB GLN C 345 " ideal model delta sigma weight residual 109.72 117.46 -7.74 1.66e+00 3.63e-01 2.17e+01 angle pdb=" C GLN B 345 " pdb=" CA GLN B 345 " pdb=" CB GLN B 345 " ideal model delta sigma weight residual 109.72 117.43 -7.71 1.66e+00 3.63e-01 2.16e+01 ... (remaining 33491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 12882 17.58 - 35.16: 1251 35.16 - 52.74: 368 52.74 - 70.33: 86 70.33 - 87.91: 29 Dihedral angle restraints: 14616 sinusoidal: 5656 harmonic: 8960 Sorted by residual: dihedral pdb=" CA GLY D 346 " pdb=" C GLY D 346 " pdb=" N VAL D 347 " pdb=" CA VAL D 347 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA GLN D 345 " pdb=" C GLN D 345 " pdb=" N GLY D 346 " pdb=" CA GLY D 346 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLY F 272 " pdb=" C GLY F 272 " pdb=" N THR F 273 " pdb=" CA THR F 273 " ideal model delta harmonic sigma weight residual 180.00 -159.31 -20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 14613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2988 0.057 - 0.114: 610 0.114 - 0.171: 68 0.171 - 0.229: 6 0.229 - 0.286: 8 Chirality restraints: 3680 Sorted by residual: chirality pdb=" CA VAL G 347 " pdb=" N VAL G 347 " pdb=" C VAL G 347 " pdb=" CB VAL G 347 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA VAL E 347 " pdb=" N VAL E 347 " pdb=" C VAL E 347 " pdb=" CB VAL E 347 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA VAL H 347 " pdb=" N VAL H 347 " pdb=" C VAL H 347 " pdb=" CB VAL H 347 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3677 not shown) Planarity restraints: 4464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 55 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.39e+00 pdb=" N PRO G 56 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO G 56 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 56 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 374 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.05e+00 pdb=" C ALA E 374 " -0.046 2.00e-02 2.50e+03 pdb=" O ALA E 374 " 0.017 2.00e-02 2.50e+03 pdb=" N THR E 375 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 374 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.04e+00 pdb=" C ALA G 374 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA G 374 " -0.017 2.00e-02 2.50e+03 pdb=" N THR G 375 " -0.016 2.00e-02 2.50e+03 ... (remaining 4461 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 412 2.69 - 3.24: 21978 3.24 - 3.80: 37678 3.80 - 4.35: 54581 4.35 - 4.90: 88592 Nonbonded interactions: 203241 Sorted by model distance: nonbonded pdb=" OQ2 KCX E 210 " pdb="ZN ZN E 501 " model vdw 2.138 2.230 nonbonded pdb=" OQ2 KCX F 210 " pdb="ZN ZN F 501 " model vdw 2.138 2.230 nonbonded pdb=" OQ2 KCX G 210 " pdb="ZN ZN G 501 " model vdw 2.139 2.230 nonbonded pdb=" OQ2 KCX H 210 " pdb="ZN ZN H 501 " model vdw 2.139 2.230 nonbonded pdb=" N GLN H 327 " pdb=" OE1 GLN H 327 " model vdw 2.216 3.120 ... (remaining 203236 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 57.560 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.130 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:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 24744 Z= 0.237 Angle : 0.669 11.066 33512 Z= 0.401 Chirality : 0.048 0.286 3680 Planarity : 0.005 0.068 4464 Dihedral : 15.866 87.908 8912 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.70 % Allowed : 15.72 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3136 helix: 0.21 (0.14), residues: 1344 sheet: -0.05 (0.24), residues: 400 loop : -0.90 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 289 HIS 0.007 0.001 HIS A 251 PHE 0.012 0.001 PHE D 294 TYR 0.008 0.001 TYR A 95 ARG 0.006 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.14509 ( 997) hydrogen bonds : angle 5.45014 ( 2820) metal coordination : bond 0.05146 ( 32) SS BOND : bond 0.00258 ( 8) SS BOND : angle 0.19980 ( 16) covalent geometry : bond 0.00373 (24704) covalent geometry : angle 0.66905 (33496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 337 time to evaluate : 2.738 Fit side-chains REVERT: E 55 LEU cc_start: 0.8051 (mm) cc_final: 0.7754 (mp) REVERT: E 331 LYS cc_start: 0.8278 (tptt) cc_final: 0.8011 (tttm) REVERT: F 55 LEU cc_start: 0.8062 (mm) cc_final: 0.7747 (mp) REVERT: F 277 ASP cc_start: 0.7809 (m-30) cc_final: 0.7472 (m-30) REVERT: G 55 LEU cc_start: 0.8039 (mm) cc_final: 0.7728 (mp) REVERT: G 277 ASP cc_start: 0.7718 (m-30) cc_final: 0.7409 (m-30) REVERT: H 55 LEU cc_start: 0.8062 (mm) cc_final: 0.7746 (mp) REVERT: H 331 LYS cc_start: 0.8376 (tttm) cc_final: 0.8017 (tptt) outliers start: 17 outliers final: 17 residues processed: 351 average time/residue: 1.5151 time to fit residues: 601.5612 Evaluate side-chains 339 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 322 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 375 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 5.9990 chunk 236 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.143846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121282 restraints weight = 23929.284| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.19 r_work: 0.3318 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 24744 Z= 0.106 Angle : 0.514 7.863 33512 Z= 0.275 Chirality : 0.044 0.136 3680 Planarity : 0.004 0.047 4464 Dihedral : 5.237 54.124 3577 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.77 % Allowed : 14.36 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3136 helix: 1.09 (0.15), residues: 1240 sheet: 0.09 (0.24), residues: 400 loop : -0.86 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 289 HIS 0.007 0.001 HIS B 251 PHE 0.012 0.001 PHE C 294 TYR 0.011 0.001 TYR C 95 ARG 0.003 0.000 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 997) hydrogen bonds : angle 4.08732 ( 2820) metal coordination : bond 0.00198 ( 32) SS BOND : bond 0.00140 ( 8) SS BOND : angle 0.13823 ( 16) covalent geometry : bond 0.00214 (24704) covalent geometry : angle 0.51426 (33496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 324 time to evaluate : 2.691 Fit side-chains REVERT: E 55 LEU cc_start: 0.8085 (mm) cc_final: 0.7843 (mp) REVERT: E 155 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7336 (mmtt) REVERT: F 55 LEU cc_start: 0.8074 (mm) cc_final: 0.7829 (mp) REVERT: F 155 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7318 (mmtt) REVERT: F 277 ASP cc_start: 0.8038 (m-30) cc_final: 0.7770 (t0) REVERT: G 55 LEU cc_start: 0.8046 (mm) cc_final: 0.7807 (mp) REVERT: G 155 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7332 (mmtt) REVERT: G 277 ASP cc_start: 0.7943 (m-30) cc_final: 0.7735 (t0) REVERT: H 55 LEU cc_start: 0.8080 (mm) cc_final: 0.7832 (mp) REVERT: H 155 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7366 (mmtt) outliers start: 43 outliers final: 30 residues processed: 337 average time/residue: 1.5381 time to fit residues: 585.9666 Evaluate side-chains 350 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 316 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 230 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 267 optimal weight: 0.0770 chunk 6 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 304 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 225 optimal weight: 9.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN C 53 GLN D 53 GLN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.138027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114809 restraints weight = 23674.707| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.19 r_work: 0.3207 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 24744 Z= 0.243 Angle : 0.674 9.714 33512 Z= 0.369 Chirality : 0.051 0.152 3680 Planarity : 0.006 0.050 4464 Dihedral : 5.571 58.700 3556 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.76 % Allowed : 13.49 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3136 helix: 0.81 (0.14), residues: 1240 sheet: -0.17 (0.24), residues: 400 loop : -1.07 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 289 HIS 0.008 0.001 HIS B 271 PHE 0.016 0.003 PHE D 294 TYR 0.015 0.002 TYR C 95 ARG 0.004 0.001 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.07729 ( 997) hydrogen bonds : angle 4.22173 ( 2820) metal coordination : bond 0.00726 ( 32) SS BOND : bond 0.00335 ( 8) SS BOND : angle 0.50702 ( 16) covalent geometry : bond 0.00567 (24704) covalent geometry : angle 0.67438 (33496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 314 time to evaluate : 2.743 Fit side-chains REVERT: A 155 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7640 (tmtm) REVERT: B 155 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7621 (tmtm) REVERT: C 155 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7628 (tmtm) REVERT: D 155 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7652 (tmtm) REVERT: E 55 LEU cc_start: 0.8111 (mm) cc_final: 0.7899 (mp) REVERT: E 98 ASP cc_start: 0.7818 (m-30) cc_final: 0.7262 (m-30) REVERT: E 155 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7387 (mmtt) REVERT: E 222 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7598 (mtm180) REVERT: F 55 LEU cc_start: 0.8117 (mm) cc_final: 0.7905 (mp) REVERT: F 155 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7377 (mmtt) REVERT: G 55 LEU cc_start: 0.8085 (mm) cc_final: 0.7878 (mp) REVERT: G 155 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7390 (mmtt) REVERT: G 222 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7585 (mtm180) REVERT: H 55 LEU cc_start: 0.8120 (mm) cc_final: 0.7905 (mp) REVERT: H 98 ASP cc_start: 0.7819 (m-30) cc_final: 0.7268 (m-30) REVERT: H 155 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7392 (mmtt) outliers start: 67 outliers final: 32 residues processed: 336 average time/residue: 1.5425 time to fit residues: 585.9859 Evaluate side-chains 347 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 305 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 72 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 279 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN C 53 GLN D 53 GLN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117885 restraints weight = 23958.198| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.19 r_work: 0.3274 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24744 Z= 0.137 Angle : 0.553 8.338 33512 Z= 0.299 Chirality : 0.046 0.141 3680 Planarity : 0.004 0.045 4464 Dihedral : 5.116 55.566 3553 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.43 % Allowed : 14.32 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3136 helix: 1.00 (0.14), residues: 1240 sheet: -0.05 (0.24), residues: 400 loop : -1.05 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 289 HIS 0.007 0.001 HIS D 251 PHE 0.013 0.002 PHE B 294 TYR 0.010 0.001 TYR B 369 ARG 0.002 0.000 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.05532 ( 997) hydrogen bonds : angle 3.98485 ( 2820) metal coordination : bond 0.00355 ( 32) SS BOND : bond 0.00151 ( 8) SS BOND : angle 0.35768 ( 16) covalent geometry : bond 0.00294 (24704) covalent geometry : angle 0.55350 (33496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 322 time to evaluate : 2.592 Fit side-chains REVERT: E 97 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: E 98 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7227 (m-30) REVERT: E 155 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7334 (mmtt) REVERT: E 222 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7575 (mtm180) REVERT: F 97 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: F 155 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7313 (mmtt) REVERT: G 97 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: G 155 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7336 (mmtt) REVERT: H 97 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: H 98 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: H 155 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7347 (mmtt) outliers start: 59 outliers final: 25 residues processed: 345 average time/residue: 1.5569 time to fit residues: 605.9967 Evaluate side-chains 351 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 315 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 259 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 34 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 223 optimal weight: 0.4980 chunk 236 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN C 53 GLN C 93 GLN C 410 ASN D 53 GLN D 93 GLN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118855 restraints weight = 23970.194| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.20 r_work: 0.3286 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24744 Z= 0.123 Angle : 0.534 8.153 33512 Z= 0.287 Chirality : 0.045 0.136 3680 Planarity : 0.004 0.045 4464 Dihedral : 4.989 52.333 3553 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.97 % Allowed : 14.27 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3136 helix: 1.16 (0.15), residues: 1240 sheet: 0.09 (0.24), residues: 400 loop : -1.03 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 289 HIS 0.007 0.001 HIS B 251 PHE 0.012 0.001 PHE B 294 TYR 0.009 0.001 TYR B 369 ARG 0.008 0.000 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.05053 ( 997) hydrogen bonds : angle 3.89648 ( 2820) metal coordination : bond 0.00289 ( 32) SS BOND : bond 0.00127 ( 8) SS BOND : angle 0.31763 ( 16) covalent geometry : bond 0.00260 (24704) covalent geometry : angle 0.53378 (33496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 314 time to evaluate : 2.959 Fit side-chains REVERT: A 97 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6944 (mm-30) REVERT: E 97 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: E 98 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7221 (m-30) REVERT: E 155 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7341 (mmtt) REVERT: F 97 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: F 155 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7352 (mmtt) REVERT: F 222 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7710 (mtm180) REVERT: G 97 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7607 (mt-10) REVERT: G 155 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7338 (mmtt) REVERT: H 97 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7610 (mt-10) REVERT: H 98 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: H 155 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7347 (mmtt) REVERT: H 222 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7688 (mtm180) outliers start: 72 outliers final: 29 residues processed: 345 average time/residue: 1.5700 time to fit residues: 612.2194 Evaluate side-chains 353 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 311 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 222 ARG Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 74 optimal weight: 6.9990 chunk 240 optimal weight: 0.9990 chunk 171 optimal weight: 0.0070 chunk 285 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 260 optimal weight: 9.9990 overall best weight: 2.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 93 GLN B 410 ASN C 53 GLN C 410 ASN D 53 GLN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.139832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116971 restraints weight = 23743.585| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.18 r_work: 0.3260 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24744 Z= 0.167 Angle : 0.591 8.835 33512 Z= 0.321 Chirality : 0.047 0.144 3680 Planarity : 0.005 0.047 4464 Dihedral : 5.209 54.270 3553 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.81 % Allowed : 14.44 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3136 helix: 1.05 (0.14), residues: 1240 sheet: 0.02 (0.24), residues: 400 loop : -1.10 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 289 HIS 0.006 0.001 HIS A 251 PHE 0.014 0.002 PHE B 294 TYR 0.012 0.002 TYR B 369 ARG 0.007 0.000 ARG H 52 Details of bonding type rmsd hydrogen bonds : bond 0.06167 ( 997) hydrogen bonds : angle 3.99203 ( 2820) metal coordination : bond 0.00462 ( 32) SS BOND : bond 0.00186 ( 8) SS BOND : angle 0.42059 ( 16) covalent geometry : bond 0.00374 (24704) covalent geometry : angle 0.59142 (33496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 312 time to evaluate : 2.792 Fit side-chains REVERT: A 97 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6836 (mm-30) REVERT: E 97 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: E 98 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7286 (m-30) REVERT: E 155 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7373 (mmtt) REVERT: F 97 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: F 155 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7358 (mmtt) REVERT: G 97 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: G 155 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7379 (mmtt) REVERT: H 97 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: H 98 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: H 155 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7382 (mmtt) outliers start: 68 outliers final: 27 residues processed: 346 average time/residue: 1.6030 time to fit residues: 624.3743 Evaluate side-chains 348 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 310 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 221 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 198 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 93 GLN B 410 ASN C 53 GLN C 410 ASN D 53 GLN D 93 GLN D 410 ASN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.137653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114346 restraints weight = 23852.557| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.20 r_work: 0.3231 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 24744 Z= 0.241 Angle : 0.676 9.654 33512 Z= 0.370 Chirality : 0.051 0.196 3680 Planarity : 0.006 0.049 4464 Dihedral : 5.515 58.090 3553 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.43 % Allowed : 14.65 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3136 helix: 0.79 (0.14), residues: 1248 sheet: -0.11 (0.24), residues: 400 loop : -1.18 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 289 HIS 0.007 0.001 HIS D 271 PHE 0.016 0.003 PHE D 294 TYR 0.015 0.002 TYR B 369 ARG 0.006 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.07620 ( 997) hydrogen bonds : angle 4.14298 ( 2820) metal coordination : bond 0.00730 ( 32) SS BOND : bond 0.00295 ( 8) SS BOND : angle 0.51196 ( 16) covalent geometry : bond 0.00559 (24704) covalent geometry : angle 0.67595 (33496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 311 time to evaluate : 2.584 Fit side-chains REVERT: A 97 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6890 (mm-30) REVERT: E 55 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7634 (mp) REVERT: E 97 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: E 98 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: E 155 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7360 (mmtt) REVERT: F 55 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7610 (mp) REVERT: F 155 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7364 (mmtt) REVERT: G 55 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7615 (mp) REVERT: G 155 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7378 (mmtt) REVERT: H 55 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7639 (mp) REVERT: H 97 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: H 98 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: H 155 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7374 (mmtt) REVERT: H 298 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7740 (mtt-85) outliers start: 59 outliers final: 29 residues processed: 333 average time/residue: 1.6147 time to fit residues: 608.2513 Evaluate side-chains 351 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 308 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 298 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 271 optimal weight: 0.9990 chunk 296 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 157 optimal weight: 0.0870 chunk 246 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 127 optimal weight: 0.4980 chunk 7 optimal weight: 6.9990 overall best weight: 0.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 93 GLN B 410 ASN C 53 GLN C 93 GLN C 410 ASN D 53 GLN D 93 GLN D 410 ASN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121812 restraints weight = 23870.445| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.19 r_work: 0.3325 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24744 Z= 0.097 Angle : 0.507 7.418 33512 Z= 0.270 Chirality : 0.044 0.157 3680 Planarity : 0.004 0.041 4464 Dihedral : 4.783 48.136 3553 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.27 % Allowed : 15.26 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3136 helix: 1.21 (0.15), residues: 1240 sheet: 0.10 (0.24), residues: 400 loop : -1.03 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 79 HIS 0.007 0.001 HIS B 251 PHE 0.010 0.001 PHE A 294 TYR 0.008 0.001 TYR G 95 ARG 0.006 0.000 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 997) hydrogen bonds : angle 3.80506 ( 2820) metal coordination : bond 0.00149 ( 32) SS BOND : bond 0.00077 ( 8) SS BOND : angle 0.26514 ( 16) covalent geometry : bond 0.00193 (24704) covalent geometry : angle 0.50709 (33496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 308 time to evaluate : 3.215 Fit side-chains REVERT: A 97 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6823 (mm-30) REVERT: E 97 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.6985 (mm-30) REVERT: E 98 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7253 (m-30) REVERT: E 155 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7323 (mmtt) REVERT: F 97 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: F 155 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7300 (mmtt) REVERT: G 97 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: G 155 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7313 (mmtt) REVERT: G 327 GLN cc_start: 0.7368 (mp10) cc_final: 0.6931 (pt0) REVERT: H 97 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.6975 (mm-30) REVERT: H 98 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: H 155 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7339 (mmtt) REVERT: H 327 GLN cc_start: 0.7301 (mp10) cc_final: 0.6908 (pt0) outliers start: 55 outliers final: 22 residues processed: 325 average time/residue: 1.6382 time to fit residues: 598.1224 Evaluate side-chains 341 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 308 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 259 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 3 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 220 optimal weight: 0.5980 chunk 206 optimal weight: 0.3980 chunk 140 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 301 optimal weight: 0.6980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 410 ASN C 53 GLN C 410 ASN D 53 GLN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117751 restraints weight = 23856.411| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.19 r_work: 0.3270 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24744 Z= 0.147 Angle : 0.571 8.541 33512 Z= 0.307 Chirality : 0.046 0.182 3680 Planarity : 0.005 0.047 4464 Dihedral : 5.088 45.245 3553 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.77 % Allowed : 16.13 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3136 helix: 1.18 (0.15), residues: 1240 sheet: 0.08 (0.24), residues: 400 loop : -1.08 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 289 HIS 0.006 0.001 HIS D 251 PHE 0.013 0.002 PHE C 294 TYR 0.011 0.001 TYR B 369 ARG 0.006 0.000 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.05619 ( 997) hydrogen bonds : angle 3.91796 ( 2820) metal coordination : bond 0.00382 ( 32) SS BOND : bond 0.00146 ( 8) SS BOND : angle 0.33952 ( 16) covalent geometry : bond 0.00324 (24704) covalent geometry : angle 0.57147 (33496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 313 time to evaluate : 2.635 Fit side-chains REVERT: A 97 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6902 (mm-30) REVERT: E 97 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.6979 (mm-30) REVERT: E 98 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: E 155 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7337 (mmtt) REVERT: F 155 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7320 (mmtt) REVERT: G 155 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7343 (mmtt) REVERT: G 331 LYS cc_start: 0.8549 (tttp) cc_final: 0.8333 (tttm) REVERT: H 97 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.6972 (mm-30) REVERT: H 98 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: H 155 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7345 (mmtt) outliers start: 43 outliers final: 24 residues processed: 330 average time/residue: 1.6266 time to fit residues: 603.1908 Evaluate side-chains 343 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 310 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 232 optimal weight: 5.9990 chunk 308 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 chunk 306 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 245 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 112 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 93 GLN B 410 ASN C 53 GLN C 410 ASN D 53 GLN D 93 GLN D 410 ASN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120469 restraints weight = 23734.976| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.19 r_work: 0.3306 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24744 Z= 0.109 Angle : 0.530 7.904 33512 Z= 0.281 Chirality : 0.044 0.170 3680 Planarity : 0.004 0.043 4464 Dihedral : 4.820 33.819 3553 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.40 % Allowed : 16.50 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3136 helix: 1.27 (0.15), residues: 1240 sheet: 0.21 (0.25), residues: 400 loop : -1.00 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 289 HIS 0.007 0.001 HIS B 251 PHE 0.012 0.001 PHE A 294 TYR 0.008 0.001 TYR A 244 ARG 0.006 0.000 ARG G 52 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 997) hydrogen bonds : angle 3.82527 ( 2820) metal coordination : bond 0.00209 ( 32) SS BOND : bond 0.00092 ( 8) SS BOND : angle 0.24160 ( 16) covalent geometry : bond 0.00224 (24704) covalent geometry : angle 0.53037 (33496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 313 time to evaluate : 2.947 Fit side-chains REVERT: A 97 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6863 (mm-30) REVERT: E 97 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.6979 (mm-30) REVERT: E 98 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: E 155 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7343 (mmtt) REVERT: E 331 LYS cc_start: 0.8466 (tttp) cc_final: 0.8241 (tttm) REVERT: F 155 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7323 (mmtt) REVERT: G 155 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7334 (mmtt) REVERT: G 327 GLN cc_start: 0.7349 (mp10) cc_final: 0.6947 (pt0) REVERT: G 331 LYS cc_start: 0.8495 (tttp) cc_final: 0.8260 (tttm) REVERT: H 97 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.6977 (mm-30) REVERT: H 98 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: H 155 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7345 (mmtt) REVERT: H 327 GLN cc_start: 0.7305 (mp10) cc_final: 0.6917 (pt0) REVERT: H 331 LYS cc_start: 0.8222 (tttm) cc_final: 0.7911 (tptt) outliers start: 34 outliers final: 24 residues processed: 325 average time/residue: 1.6813 time to fit residues: 615.5767 Evaluate side-chains 346 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 313 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 298 optimal weight: 0.7980 chunk 258 optimal weight: 2.9990 chunk 303 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 255 optimal weight: 0.3980 chunk 289 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 93 GLN B 410 ASN C 53 GLN C 93 GLN C 410 ASN D 53 GLN D 410 ASN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118081 restraints weight = 23731.401| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.19 r_work: 0.3276 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24744 Z= 0.143 Angle : 0.573 8.495 33512 Z= 0.307 Chirality : 0.046 0.192 3680 Planarity : 0.004 0.046 4464 Dihedral : 5.021 34.752 3553 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.73 % Allowed : 16.38 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3136 helix: 1.19 (0.15), residues: 1240 sheet: 0.14 (0.24), residues: 400 loop : -1.05 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 289 HIS 0.006 0.001 HIS D 251 PHE 0.013 0.002 PHE C 294 TYR 0.011 0.001 TYR B 369 ARG 0.005 0.000 ARG G 52 Details of bonding type rmsd hydrogen bonds : bond 0.05500 ( 997) hydrogen bonds : angle 3.90210 ( 2820) metal coordination : bond 0.00362 ( 32) SS BOND : bond 0.00138 ( 8) SS BOND : angle 0.34023 ( 16) covalent geometry : bond 0.00314 (24704) covalent geometry : angle 0.57317 (33496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17731.10 seconds wall clock time: 304 minutes 54.29 seconds (18294.29 seconds total)