Starting phenix.real_space_refine on Mon Aug 25 01:00:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihr_35453/08_2025/8ihr_35453.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihr_35453/08_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_35453/08_2025/8ihr_35453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihr_35453/08_2025/8ihr_35453.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihr_35453/08_2025/8ihr_35453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihr_35453/08_2025/8ihr_35453.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.065 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.20, per 1000 atoms: 0.21 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: 1.90 Conformation dependent library (CDL) restraints added in 884.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.54 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: 4.30 Time building geometry restraints manager: 2.57 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: 0.03 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 22.380 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:9.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.180 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (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 ARG 0.006 0.000 ARG E 52 TYR 0.008 0.001 TYR A 95 PHE 0.012 0.001 PHE D 294 TRP 0.005 0.001 TRP E 289 HIS 0.007 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00373 (24704) covalent geometry : angle 0.66905 (33496) SS BOND : bond 0.00258 ( 8) SS BOND : angle 0.19980 ( 16) hydrogen bonds : bond 0.14509 ( 997) hydrogen bonds : angle 5.45014 ( 2820) metal coordination : bond 0.05146 ( 32) *********************** 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 : 0.775 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: 0.8088 time to fit residues: 319.6433 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 : 1.006 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.0980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.141921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118868 restraints weight = 23985.414| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.20 r_work: 0.3289 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 24744 Z= 0.130 Angle : 0.546 8.214 33512 Z= 0.295 Chirality : 0.045 0.141 3680 Planarity : 0.004 0.048 4464 Dihedral : 5.476 55.954 3577 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.94 % Allowed : 14.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.15), residues: 3136 helix: 1.01 (0.15), residues: 1240 sheet: 0.00 (0.24), residues: 400 loop : -0.90 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 52 TYR 0.012 0.001 TYR C 95 PHE 0.013 0.002 PHE C 294 TRP 0.005 0.001 TRP E 289 HIS 0.007 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00275 (24704) covalent geometry : angle 0.54660 (33496) SS BOND : bond 0.00181 ( 8) SS BOND : angle 0.17682 ( 16) hydrogen bonds : bond 0.05449 ( 997) hydrogen bonds : angle 4.14443 ( 2820) metal coordination : bond 0.00325 ( 32) *********************** 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 372 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 325 time to evaluate : 1.030 Fit side-chains REVERT: E 55 LEU cc_start: 0.8039 (mm) cc_final: 0.7807 (mp) REVERT: E 155 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7306 (mmtt) REVERT: F 55 LEU cc_start: 0.8056 (mm) cc_final: 0.7818 (mp) REVERT: F 155 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7285 (mmtt) REVERT: F 222 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7198 (mtm180) REVERT: F 277 ASP cc_start: 0.8072 (m-30) cc_final: 0.7796 (t0) REVERT: G 55 LEU cc_start: 0.8035 (mm) cc_final: 0.7799 (mp) REVERT: G 155 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7300 (mmtt) REVERT: G 277 ASP cc_start: 0.8002 (m-30) cc_final: 0.7775 (t0) REVERT: H 55 LEU cc_start: 0.8061 (mm) cc_final: 0.7822 (mp) REVERT: H 155 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7330 (mmtt) REVERT: H 222 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7207 (mtm180) outliers start: 47 outliers final: 30 residues processed: 337 average time/residue: 0.8280 time to fit residues: 313.9004 Evaluate side-chains 353 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 317 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 222 ARG 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 222 ARG 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 273 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 289 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.141906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119115 restraints weight = 24007.718| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.20 r_work: 0.3289 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.0741 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= 0.127 Angle : 0.536 8.196 33512 Z= 0.289 Chirality : 0.045 0.136 3680 Planarity : 0.004 0.044 4464 Dihedral : 5.078 53.258 3556 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.48 % Allowed : 14.07 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.14), residues: 3136 helix: 1.11 (0.15), residues: 1240 sheet: 0.05 (0.24), residues: 400 loop : -0.94 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 52 TYR 0.010 0.001 TYR C 95 PHE 0.013 0.002 PHE C 294 TRP 0.005 0.001 TRP H 289 HIS 0.007 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00270 (24704) covalent geometry : angle 0.53658 (33496) SS BOND : bond 0.00134 ( 8) SS BOND : angle 0.26067 ( 16) hydrogen bonds : bond 0.05260 ( 997) hydrogen bonds : angle 3.98155 ( 2820) metal coordination : bond 0.00309 ( 32) *********************** 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 379 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 319 time to evaluate : 0.894 Fit side-chains REVERT: E 55 LEU cc_start: 0.8190 (mm) cc_final: 0.7960 (mp) REVERT: E 155 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7330 (mmtt) REVERT: F 55 LEU cc_start: 0.8166 (mm) cc_final: 0.7932 (mp) REVERT: F 155 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7315 (mmtt) REVERT: G 55 LEU cc_start: 0.8168 (mm) cc_final: 0.7941 (mp) REVERT: G 155 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7328 (mmtt) REVERT: H 55 LEU cc_start: 0.8176 (mm) cc_final: 0.7939 (mp) REVERT: H 155 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7347 (mmtt) outliers start: 60 outliers final: 29 residues processed: 338 average time/residue: 0.8253 time to fit residues: 313.6617 Evaluate side-chains 347 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 314 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 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 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 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 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 204 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 chunk 229 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 240 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 308 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.138423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.115212 restraints weight = 23919.137| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.20 r_work: 0.3238 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 24744 Z= 0.219 Angle : 0.646 9.465 33512 Z= 0.353 Chirality : 0.050 0.150 3680 Planarity : 0.005 0.049 4464 Dihedral : 5.383 56.987 3553 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.60 % Allowed : 14.44 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.14), residues: 3136 helix: 0.91 (0.14), residues: 1240 sheet: -0.06 (0.24), residues: 400 loop : -1.09 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 52 TYR 0.014 0.002 TYR C 369 PHE 0.015 0.002 PHE D 294 TRP 0.009 0.002 TRP G 289 HIS 0.007 0.001 HIS C 271 Details of bonding type rmsd covalent geometry : bond 0.00504 (24704) covalent geometry : angle 0.64630 (33496) SS BOND : bond 0.00283 ( 8) SS BOND : angle 0.54703 ( 16) hydrogen bonds : bond 0.07247 ( 997) hydrogen bonds : angle 4.13867 ( 2820) metal coordination : bond 0.00650 ( 32) *********************** 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 378 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 315 time to evaluate : 1.029 Fit side-chains REVERT: E 97 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: E 98 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7292 (m-30) REVERT: E 155 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7398 (mmtt) REVERT: F 97 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: F 155 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7404 (mmtt) REVERT: G 97 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: G 155 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7413 (mmtt) REVERT: H 97 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: H 98 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7291 (m-30) REVERT: H 155 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7414 (mmtt) outliers start: 63 outliers final: 33 residues processed: 340 average time/residue: 0.8358 time to fit residues: 319.3436 Evaluate side-chains 354 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 311 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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 208 LEU 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 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 208 LEU 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 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 284 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 192 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 237 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.143905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121477 restraints weight = 23913.133| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.19 r_work: 0.3319 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24744 Z= 0.096 Angle : 0.501 7.465 33512 Z= 0.265 Chirality : 0.043 0.133 3680 Planarity : 0.004 0.042 4464 Dihedral : 4.787 47.321 3553 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.76 % Allowed : 14.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.15), residues: 3136 helix: 1.22 (0.15), residues: 1240 sheet: 0.16 (0.24), residues: 400 loop : -0.96 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 52 TYR 0.008 0.001 TYR G 95 PHE 0.011 0.001 PHE F 294 TRP 0.004 0.001 TRP B 79 HIS 0.007 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00188 (24704) covalent geometry : angle 0.50095 (33496) SS BOND : bond 0.00086 ( 8) SS BOND : angle 0.26925 ( 16) hydrogen bonds : bond 0.04126 ( 997) hydrogen bonds : angle 3.83510 ( 2820) metal coordination : bond 0.00150 ( 32) *********************** 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 378 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 311 time to evaluate : 0.969 Fit side-chains REVERT: E 55 LEU cc_start: 0.8170 (mm) cc_final: 0.7822 (mp) REVERT: E 97 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: E 98 ASP cc_start: 0.7725 (m-30) cc_final: 0.7167 (m-30) REVERT: E 155 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7316 (mmtt) REVERT: F 55 LEU cc_start: 0.8196 (mm) cc_final: 0.7887 (mp) REVERT: F 97 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: F 155 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7307 (mmtt) REVERT: G 55 LEU cc_start: 0.8150 (mm) cc_final: 0.7813 (mp) REVERT: G 97 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: G 155 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7319 (mmtt) REVERT: H 55 LEU cc_start: 0.8193 (mm) cc_final: 0.7877 (mp) REVERT: H 97 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: H 98 ASP cc_start: 0.7740 (m-30) cc_final: 0.7184 (m-30) REVERT: H 155 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7335 (mmtt) REVERT: H 283 MET cc_start: 0.8746 (mtp) cc_final: 0.8541 (mtp) outliers start: 67 outliers final: 29 residues processed: 343 average time/residue: 0.7421 time to fit residues: 286.0592 Evaluate side-chains 349 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 312 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 326 SER 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 288 THR Chi-restraints excluded: chain D residue 326 SER 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 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 155 LYS 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 161 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 275 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 304 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 271 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 D 93 GLN D 345 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 = 0.3568 r_free = 0.3568 target = 0.137246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113898 restraints weight = 23840.095| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.20 r_work: 0.3224 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 24744 Z= 0.272 Angle : 0.709 9.826 33512 Z= 0.388 Chirality : 0.053 0.198 3680 Planarity : 0.006 0.049 4464 Dihedral : 5.546 58.819 3553 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.01 % Allowed : 14.32 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.14), residues: 3136 helix: 0.79 (0.14), residues: 1248 sheet: -0.09 (0.24), residues: 400 loop : -1.16 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 195 TYR 0.016 0.003 TYR B 369 PHE 0.018 0.003 PHE B 294 TRP 0.011 0.002 TRP G 289 HIS 0.008 0.002 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00638 (24704) covalent geometry : angle 0.70929 (33496) SS BOND : bond 0.00379 ( 8) SS BOND : angle 0.57557 ( 16) hydrogen bonds : bond 0.08028 ( 997) hydrogen bonds : angle 4.18233 ( 2820) metal coordination : bond 0.00826 ( 32) *********************** 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 376 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 303 time to evaluate : 0.921 Fit side-chains REVERT: A 97 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6995 (mm-30) REVERT: D 278 GLU cc_start: 0.7869 (tt0) cc_final: 0.7598 (tt0) REVERT: E 97 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: E 98 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: E 155 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7384 (mmtt) REVERT: F 155 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7375 (mmtt) REVERT: F 298 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7727 (mtt-85) REVERT: G 55 LEU cc_start: 0.8106 (mm) cc_final: 0.7812 (mp) REVERT: G 97 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: G 155 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7383 (mmtt) REVERT: H 97 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: H 98 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7342 (m-30) REVERT: H 155 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7396 (mmtt) outliers start: 73 outliers final: 31 residues processed: 342 average time/residue: 0.7937 time to fit residues: 304.6962 Evaluate side-chains 344 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 302 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 326 SER 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 326 SER 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 326 SER 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 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 298 ARG 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 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 81 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 212 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 E 53 GLN F 37 GLN F 53 GLN G 37 GLN H 37 GLN H 53 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115829 restraints weight = 23710.443| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.18 r_work: 0.3244 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 24744 Z= 0.204 Angle : 0.642 9.238 33512 Z= 0.349 Chirality : 0.049 0.191 3680 Planarity : 0.005 0.049 4464 Dihedral : 5.429 57.914 3553 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.56 % Allowed : 14.89 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.14), residues: 3136 helix: 0.84 (0.14), residues: 1240 sheet: -0.16 (0.24), residues: 400 loop : -1.21 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 52 TYR 0.013 0.002 TYR C 369 PHE 0.014 0.002 PHE D 294 TRP 0.009 0.002 TRP G 289 HIS 0.007 0.001 HIS D 271 Details of bonding type rmsd covalent geometry : bond 0.00466 (24704) covalent geometry : angle 0.64163 (33496) SS BOND : bond 0.00237 ( 8) SS BOND : angle 0.47655 ( 16) hydrogen bonds : bond 0.06886 ( 997) hydrogen bonds : angle 4.07114 ( 2820) metal coordination : bond 0.00592 ( 32) *********************** 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 363 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 301 time to evaluate : 0.991 Fit side-chains REVERT: A 97 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6987 (mm-30) REVERT: D 278 GLU cc_start: 0.7842 (tt0) cc_final: 0.7578 (tt0) REVERT: E 97 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: E 98 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: E 155 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7351 (mmtt) REVERT: F 55 LEU cc_start: 0.7933 (mm) cc_final: 0.7659 (mp) REVERT: F 97 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: F 155 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7353 (mmtt) REVERT: F 298 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7776 (mtt-85) REVERT: G 55 LEU cc_start: 0.8075 (mm) cc_final: 0.7797 (mp) REVERT: G 155 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7364 (mmtt) REVERT: G 222 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7647 (mtm180) REVERT: H 55 LEU cc_start: 0.7938 (mm) cc_final: 0.7663 (mp) REVERT: H 97 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: H 98 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7309 (m-30) REVERT: H 155 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7367 (mmtt) REVERT: H 298 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7704 (mtt-85) outliers start: 62 outliers final: 33 residues processed: 328 average time/residue: 0.7971 time to fit residues: 293.7299 Evaluate side-chains 341 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 295 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 326 SER 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 326 SER Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 326 SER 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 F residue 298 ARG 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 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 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 Chi-restraints excluded: chain H residue 298 ARG Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 183 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 262 optimal weight: 0.0980 chunk 1 optimal weight: 5.9990 chunk 160 optimal weight: 0.0020 chunk 118 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.142393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119777 restraints weight = 23735.885| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.19 r_work: 0.3296 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.0901 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= 0.112 Angle : 0.533 7.970 33512 Z= 0.285 Chirality : 0.045 0.167 3680 Planarity : 0.004 0.045 4464 Dihedral : 4.970 51.319 3553 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.31 % Allowed : 15.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.14), residues: 3136 helix: 1.12 (0.15), residues: 1240 sheet: 0.01 (0.24), residues: 400 loop : -1.07 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 52 TYR 0.009 0.001 TYR A 95 PHE 0.011 0.001 PHE A 294 TRP 0.004 0.001 TRP B 79 HIS 0.007 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00231 (24704) covalent geometry : angle 0.53331 (33496) SS BOND : bond 0.00095 ( 8) SS BOND : angle 0.29788 ( 16) hydrogen bonds : bond 0.04711 ( 997) hydrogen bonds : angle 3.85668 ( 2820) metal coordination : bond 0.00246 ( 32) *********************** 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 365 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 309 time to evaluate : 0.917 Fit side-chains REVERT: A 97 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6893 (mm-30) REVERT: D 277 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7340 (t0) REVERT: D 278 GLU cc_start: 0.7833 (tt0) cc_final: 0.7567 (tt0) REVERT: E 97 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.6941 (mm-30) REVERT: E 98 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7261 (m-30) REVERT: E 155 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7333 (mmtt) REVERT: F 55 LEU cc_start: 0.7984 (mm) cc_final: 0.7749 (mp) REVERT: F 97 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: F 155 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7313 (mmtt) REVERT: G 55 LEU cc_start: 0.8066 (mm) cc_final: 0.7807 (mp) REVERT: G 155 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7324 (mmtt) REVERT: H 55 LEU cc_start: 0.8003 (mm) cc_final: 0.7764 (mp) REVERT: H 97 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6936 (mm-30) REVERT: H 98 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: H 155 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7340 (mmtt) outliers start: 56 outliers final: 28 residues processed: 333 average time/residue: 0.8181 time to fit residues: 305.2606 Evaluate side-chains 347 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 308 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 326 SER 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 326 SER 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 326 SER 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 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 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 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 22 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.138457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.115293 restraints weight = 23785.987| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.19 r_work: 0.3209 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24744 Z= 0.218 Angle : 0.656 9.391 33512 Z= 0.356 Chirality : 0.050 0.211 3680 Planarity : 0.005 0.049 4464 Dihedral : 5.426 57.148 3553 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.15 % Allowed : 15.59 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.14), residues: 3136 helix: 0.87 (0.14), residues: 1248 sheet: -0.10 (0.24), residues: 400 loop : -1.16 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 52 TYR 0.014 0.002 TYR D 369 PHE 0.015 0.002 PHE B 294 TRP 0.009 0.002 TRP G 289 HIS 0.007 0.001 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00503 (24704) covalent geometry : angle 0.65560 (33496) SS BOND : bond 0.00272 ( 8) SS BOND : angle 0.47383 ( 16) hydrogen bonds : bond 0.07134 ( 997) hydrogen bonds : angle 4.07410 ( 2820) metal coordination : bond 0.00613 ( 32) *********************** 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 354 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 302 time to evaluate : 0.999 Fit side-chains REVERT: A 97 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6977 (mm-30) REVERT: D 278 GLU cc_start: 0.7894 (tt0) cc_final: 0.7628 (tt0) REVERT: E 55 LEU cc_start: 0.7977 (mm) cc_final: 0.7643 (mp) REVERT: E 98 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: E 155 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7402 (mmtt) REVERT: F 155 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7390 (mmtt) REVERT: G 55 LEU cc_start: 0.8054 (mm) cc_final: 0.7788 (mp) REVERT: G 155 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7408 (mmtt) REVERT: H 98 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: H 155 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7417 (mmtt) outliers start: 52 outliers final: 32 residues processed: 324 average time/residue: 0.8525 time to fit residues: 309.4097 Evaluate side-chains 336 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 326 SER 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 326 SER 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 326 SER Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL 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 155 LYS 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 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 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 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 182 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.139993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116991 restraints weight = 23700.891| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.19 r_work: 0.3266 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24744 Z= 0.161 Angle : 0.599 8.682 33512 Z= 0.323 Chirality : 0.047 0.198 3680 Planarity : 0.005 0.047 4464 Dihedral : 5.249 54.445 3553 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.94 % Allowed : 15.76 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.14), residues: 3136 helix: 0.98 (0.14), residues: 1240 sheet: -0.07 (0.24), residues: 400 loop : -1.17 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 52 TYR 0.012 0.002 TYR D 369 PHE 0.013 0.002 PHE D 294 TRP 0.007 0.001 TRP E 289 HIS 0.007 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00358 (24704) covalent geometry : angle 0.59897 (33496) SS BOND : bond 0.00164 ( 8) SS BOND : angle 0.37471 ( 16) hydrogen bonds : bond 0.06003 ( 997) hydrogen bonds : angle 3.97026 ( 2820) metal coordination : bond 0.00430 ( 32) ********************** 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 350 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 303 time to evaluate : 1.000 Fit side-chains REVERT: A 97 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6998 (mm-30) REVERT: D 277 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7462 (t0) REVERT: D 278 GLU cc_start: 0.7840 (tt0) cc_final: 0.7581 (tt0) REVERT: E 55 LEU cc_start: 0.7968 (mm) cc_final: 0.7726 (mp) REVERT: E 98 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7293 (m-30) REVERT: E 155 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7360 (mmtt) REVERT: E 331 LYS cc_start: 0.8507 (tttp) cc_final: 0.8287 (tttm) REVERT: F 155 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7350 (mmtt) REVERT: G 55 LEU cc_start: 0.8042 (mm) cc_final: 0.7798 (mp) REVERT: G 155 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7374 (mmtt) REVERT: H 98 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7297 (m-30) REVERT: H 155 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7383 (mmtt) outliers start: 47 outliers final: 30 residues processed: 322 average time/residue: 0.8074 time to fit residues: 293.2576 Evaluate side-chains 342 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 304 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 326 SER Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 326 SER 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 326 SER Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL 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 155 LYS 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 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 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 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 220 optimal weight: 4.9990 chunk 229 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 282 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3612 r_free = 0.3612 target = 0.140823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.117899 restraints weight = 23795.484| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.18 r_work: 0.3266 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 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 0.039 24744 Z= 0.142 Angle : 0.577 8.423 33512 Z= 0.309 Chirality : 0.046 0.197 3680 Planarity : 0.005 0.047 4464 Dihedral : 5.142 52.901 3553 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.94 % Allowed : 15.84 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.14), residues: 3136 helix: 1.06 (0.14), residues: 1240 sheet: -0.04 (0.24), residues: 400 loop : -1.13 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 52 TYR 0.011 0.001 TYR D 369 PHE 0.013 0.002 PHE C 294 TRP 0.006 0.001 TRP E 289 HIS 0.007 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00310 (24704) covalent geometry : angle 0.57751 (33496) SS BOND : bond 0.00135 ( 8) SS BOND : angle 0.33296 ( 16) hydrogen bonds : bond 0.05512 ( 997) hydrogen bonds : angle 3.91890 ( 2820) metal coordination : bond 0.00349 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9229.30 seconds wall clock time: 157 minutes 45.84 seconds (9465.84 seconds total)