Starting phenix.real_space_refine on Fri Sep 19 08:20:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihs_35454/09_2025/8ihs_35454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihs_35454/09_2025/8ihs_35454.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 { model { file = "/net/cci-nas-00/data/ceres_data/8ihs_35454/09_2025/8ihs_35454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihs_35454/09_2025/8ihs_35454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ihs_35454/09_2025/8ihs_35454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihs_35454/09_2025/8ihs_35454.map" } 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= 0.001 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 16 6.06 5 S 72 5.16 5 Cl 8 4.86 5 C 15272 2.51 5 N 4432 2.21 5 O 4552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24352 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 5.90, per 1000 atoms: 0.24 Number of scatterers: 24352 At special positions: 0 Unit cell: (147.05, 147.05, 102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 16 29.99 Cl 8 17.00 S 72 16.00 O 4552 8.00 N 4432 7.00 C 15272 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=2.04 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.04 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.04 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.04 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.04 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.04 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 75 " distance=2.04 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 75 " distance=2.04 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: 2.16 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 85 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 83 " 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 85 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 83 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 251 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 271 " 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=" NE2 HIS C 271 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 251 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 85 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 83 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 251 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 271 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 85 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 83 " 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 85 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 83 " 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 85 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 83 " 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: 120 helices and 32 sheets defined 41.1% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 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 244 removed outlier: 3.583A pdb=" N ASP A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) 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 303 removed outlier: 3.724A pdb=" N GLY A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 removed outlier: 3.626A pdb=" N GLY A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.547A pdb=" N THR A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.983A pdb=" N VAL A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 373 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.601A 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 102 through 120 removed outlier: 3.545A pdb=" N HIS B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 142 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: 3.584A pdb=" N ASP B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 3.725A 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 303 removed outlier: 3.724A pdb=" N GLY B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 removed outlier: 3.626A pdb=" N GLY B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 363 removed outlier: 3.982A pdb=" N VAL B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 373 Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.601A pdb=" N ALA B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'C' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 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: 3.583A pdb=" N ASP C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 3.725A 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 303 removed outlier: 3.723A pdb=" N GLY C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.547A pdb=" N THR C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 363 removed outlier: 3.983A pdb=" N VAL C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 373 Processing helix chain 'C' and resid 375 through 383 removed outlier: 3.601A pdb=" N ALA C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 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: 3.583A pdb=" N ASP D 243 " --> pdb=" O ASP D 239 " (cutoff:3.500A) removed outlier: 3.725A 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 303 removed outlier: 3.724A pdb=" N GLY D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 363 removed outlier: 3.982A pdb=" N VAL D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 373 Processing helix chain 'D' and resid 375 through 383 removed outlier: 3.601A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 142 Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 182 through 186 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP E 243 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 3.725A 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 303 removed outlier: 3.724A pdb=" N GLY E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 322 removed outlier: 3.626A pdb=" N GLY E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.547A pdb=" N THR E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 363 removed outlier: 3.983A pdb=" N VAL E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 373 Processing helix chain 'E' and resid 375 through 383 Processing helix chain 'E' and resid 408 through 413 Processing helix chain 'F' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 142 Processing helix chain 'F' and resid 171 through 179 Processing helix chain 'F' and resid 182 through 186 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP F 243 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 3.726A 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 303 removed outlier: 3.724A pdb=" N GLY F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR F 328 " --> pdb=" O LEU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 removed outlier: 3.982A pdb=" N VAL F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 373 Processing helix chain 'F' and resid 375 through 383 Processing helix chain 'F' and resid 408 through 413 Processing helix chain 'G' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 Processing helix chain 'G' and resid 171 through 179 Processing helix chain 'G' and resid 182 through 186 Processing helix chain 'G' and resid 190 through 204 Processing helix chain 'G' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP G 243 " --> pdb=" O ASP G 239 " (cutoff:3.500A) removed outlier: 3.725A 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 303 removed outlier: 3.723A pdb=" N GLY G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY G 322 " --> pdb=" O ALA G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR G 328 " --> pdb=" O LEU G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 363 removed outlier: 3.983A pdb=" N VAL G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 373 Processing helix chain 'G' and resid 375 through 383 Processing helix chain 'G' and resid 408 through 413 Processing helix chain 'H' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS H 106 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 142 Processing helix chain 'H' and resid 171 through 179 Processing helix chain 'H' and resid 182 through 186 Processing helix chain 'H' and resid 190 through 204 Processing helix chain 'H' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP H 243 " --> pdb=" O ASP H 239 " (cutoff:3.500A) removed outlier: 3.724A 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 303 removed outlier: 3.724A pdb=" N GLY H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR H 328 " --> pdb=" O LEU H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 363 removed outlier: 3.982A pdb=" N VAL H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 373 Processing helix chain 'H' and resid 375 through 383 Processing helix chain 'H' and resid 408 through 413 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38 removed outlier: 6.344A pdb=" N THR A 43 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 54 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 45 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 removed outlier: 13.872A pdb=" N VAL A 23 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY A 71 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL A 25 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS A 73 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS A 27 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS A 75 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG A 29 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N PHE A 31 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 418 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing sheet with id=AA3, 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: 8.307A pdb=" N ARG A 126 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP A 81 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 212 removed outlier: 6.987A pdb=" N VAL A 248 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N GLU A 270 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA A 250 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 269 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.622A pdb=" N THR B 43 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL B 54 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU B 45 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 38 removed outlier: 13.872A pdb=" N VAL B 23 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY B 71 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL B 25 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS B 73 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS B 27 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS B 75 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG B 29 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE B 31 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL B 418 " --> pdb=" O TYR B 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP B 79 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG B 126 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP B 81 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.653A pdb=" N ILE B 209 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N HIS B 251 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE B 211 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 248 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU B 270 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA B 250 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 269 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 38 removed outlier: 6.622A pdb=" N THR C 43 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL C 54 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU C 45 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 38 removed outlier: 13.873A pdb=" N VAL C 23 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY C 71 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL C 25 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS C 73 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS C 27 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS C 75 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG C 29 " --> pdb=" O CYS C 75 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE C 31 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL C 418 " --> pdb=" O TYR C 425 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP C 79 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG C 126 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP C 81 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 209 through 212 removed outlier: 6.675A pdb=" N ILE C 209 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS C 251 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE C 211 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL C 248 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N GLU C 270 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA C 250 " --> pdb=" O GLU C 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE C 269 " --> pdb=" O VAL C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 37 through 38 removed outlier: 6.623A pdb=" N THR D 43 " --> pdb=" O VAL D 54 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL D 54 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU D 45 " --> pdb=" O ARG D 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 37 through 38 removed outlier: 13.873A pdb=" N VAL D 23 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY D 71 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 12.718A pdb=" N VAL D 25 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS D 73 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS D 27 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS D 75 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG D 29 " --> pdb=" O CYS D 75 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE D 31 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 418 " --> pdb=" O TYR D 425 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP D 79 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG D 126 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP D 81 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 209 through 212 removed outlier: 6.675A pdb=" N ILE D 209 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS D 251 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE D 211 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL D 248 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU D 270 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA D 250 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE D 269 " --> pdb=" O VAL D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 37 through 38 removed outlier: 6.622A pdb=" N THR E 43 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL E 54 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU E 45 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 37 through 38 removed outlier: 13.872A pdb=" N VAL E 23 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY E 71 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL E 25 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS E 73 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS E 27 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N CYS E 75 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG E 29 " --> pdb=" O CYS E 75 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N PHE E 31 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE E 417 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 418 " --> pdb=" O TYR E 425 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP E 79 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG E 126 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP E 81 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 209 through 212 removed outlier: 6.675A pdb=" N ILE E 209 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS E 251 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE E 211 " --> pdb=" O HIS E 251 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL E 248 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU E 270 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA E 250 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE E 269 " --> pdb=" O VAL E 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 37 through 38 removed outlier: 6.621A pdb=" N THR F 43 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL F 54 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU F 45 " --> pdb=" O ARG F 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 37 through 38 removed outlier: 13.873A pdb=" N VAL F 23 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY F 71 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 12.718A pdb=" N VAL F 25 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS F 73 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS F 27 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS F 75 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG F 29 " --> pdb=" O CYS F 75 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N PHE F 31 " --> pdb=" O PRO F 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE F 417 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL F 418 " --> pdb=" O TYR F 425 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP F 79 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ARG F 126 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP F 81 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 209 through 212 removed outlier: 6.675A pdb=" N ILE F 209 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS F 251 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE F 211 " --> pdb=" O HIS F 251 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL F 248 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU F 270 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA F 250 " --> pdb=" O GLU F 270 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE F 269 " --> pdb=" O VAL F 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 37 through 38 removed outlier: 6.622A pdb=" N THR G 43 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL G 54 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU G 45 " --> pdb=" O ARG G 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 37 through 38 removed outlier: 13.872A pdb=" N VAL G 23 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY G 71 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 12.720A pdb=" N VAL G 25 " --> pdb=" O GLY G 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS G 73 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS G 27 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS G 75 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG G 29 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N PHE G 31 " --> pdb=" O PRO G 77 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE G 417 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL G 418 " --> pdb=" O TYR G 425 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP G 79 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG G 126 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP G 81 " --> pdb=" O ARG G 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 209 through 212 removed outlier: 6.675A pdb=" N ILE G 209 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS G 251 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE G 211 " --> pdb=" O HIS G 251 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL G 248 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU G 270 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA G 250 " --> pdb=" O GLU G 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE G 269 " --> pdb=" O VAL G 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 37 through 38 removed outlier: 6.623A pdb=" N THR H 43 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL H 54 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU H 45 " --> pdb=" O ARG H 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 37 through 38 removed outlier: 13.873A pdb=" N VAL H 23 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY H 71 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL H 25 " --> pdb=" O GLY H 71 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N LYS H 73 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS H 27 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS H 75 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG H 29 " --> pdb=" O CYS H 75 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE H 31 " --> pdb=" O PRO H 77 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE H 417 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL H 418 " --> pdb=" O TYR H 425 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP H 79 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG H 126 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP H 81 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 209 through 212 removed outlier: 6.675A pdb=" N ILE H 209 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS H 251 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE H 211 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL H 248 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLU H 270 " --> pdb=" O VAL H 248 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA H 250 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE H 269 " --> pdb=" O VAL H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 999 hydrogen bonds defined for protein. 2685 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: 5.06 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8421 1.34 - 1.46: 5485 1.46 - 1.58: 10806 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 24848 Sorted by residual: bond pdb=" CB 97U A 503 " pdb=" CG 97U A 503 " ideal model delta sigma weight residual 1.505 1.384 0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" CB 97U F 503 " pdb=" CG 97U F 503 " ideal model delta sigma weight residual 1.505 1.384 0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" CB 97U G 503 " pdb=" CG 97U G 503 " ideal model delta sigma weight residual 1.505 1.385 0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CB 97U E 503 " pdb=" CG 97U E 503 " ideal model delta sigma weight residual 1.505 1.386 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" CB 97U B 503 " pdb=" CG 97U B 503 " ideal model delta sigma weight residual 1.505 1.386 0.119 2.00e-02 2.50e+03 3.56e+01 ... (remaining 24843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 33328 2.63 - 5.25: 343 5.25 - 7.88: 41 7.88 - 10.51: 0 10.51 - 13.13: 8 Bond angle restraints: 33720 Sorted by residual: angle pdb=" CAH 97U D 503 " pdb=" OAI 97U D 503 " pdb=" CAJ 97U D 503 " ideal model delta sigma weight residual 120.79 107.66 13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CAH 97U C 503 " pdb=" OAI 97U C 503 " pdb=" CAJ 97U C 503 " ideal model delta sigma weight residual 120.79 107.68 13.11 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CAH 97U A 503 " pdb=" OAI 97U A 503 " pdb=" CAJ 97U A 503 " ideal model delta sigma weight residual 120.79 107.71 13.08 3.00e+00 1.11e-01 1.90e+01 angle pdb=" CAH 97U B 503 " pdb=" OAI 97U B 503 " pdb=" CAJ 97U B 503 " ideal model delta sigma weight residual 120.79 107.81 12.98 3.00e+00 1.11e-01 1.87e+01 angle pdb=" N THR H 301 " pdb=" CA THR H 301 " pdb=" C THR H 301 " ideal model delta sigma weight residual 113.55 108.10 5.45 1.26e+00 6.30e-01 1.87e+01 ... (remaining 33715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 12769 17.83 - 35.65: 1457 35.65 - 53.48: 424 53.48 - 71.30: 77 71.30 - 89.12: 73 Dihedral angle restraints: 14800 sinusoidal: 5840 harmonic: 8960 Sorted by residual: dihedral pdb=" CB CYS G 27 " pdb=" SG CYS G 27 " pdb=" SG CYS G 75 " pdb=" CB CYS G 75 " ideal model delta sinusoidal sigma weight residual 93.00 15.14 77.86 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS E 27 " pdb=" SG CYS E 27 " pdb=" SG CYS E 75 " pdb=" CB CYS E 75 " ideal model delta sinusoidal sigma weight residual 93.00 15.17 77.83 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS A 27 " pdb=" SG CYS A 27 " pdb=" SG CYS A 75 " pdb=" CB CYS A 75 " ideal model delta sinusoidal sigma weight residual 93.00 15.17 77.83 1 1.00e+01 1.00e-02 7.58e+01 ... (remaining 14797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3291 0.073 - 0.146: 377 0.146 - 0.219: 12 0.219 - 0.292: 0 0.292 - 0.364: 8 Chirality restraints: 3688 Sorted by residual: chirality pdb=" CA 97U H 503 " pdb=" N 97U H 503 " pdb=" C 97U H 503 " pdb=" CB 97U H 503 " both_signs ideal model delta sigma weight residual False 2.30 2.67 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA 97U G 503 " pdb=" N 97U G 503 " pdb=" C 97U G 503 " pdb=" CB 97U G 503 " both_signs ideal model delta sigma weight residual False 2.30 2.66 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA 97U E 503 " pdb=" N 97U E 503 " pdb=" C 97U E 503 " pdb=" CB 97U E 503 " both_signs ideal model delta sigma weight residual False 2.30 2.66 -0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3685 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG G 298 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C ARG G 298 " 0.033 2.00e-02 2.50e+03 pdb=" O ARG G 298 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE G 299 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 102 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO G 103 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 103 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 103 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 291 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO G 292 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 292 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 292 " -0.023 5.00e-02 4.00e+02 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 23 2.15 - 2.84: 7699 2.84 - 3.52: 30872 3.52 - 4.21: 58985 4.21 - 4.90: 105021 Nonbonded interactions: 202600 Sorted by model distance: nonbonded pdb="ZN ZN C 502 " pdb=" OAX 97U C 503 " model vdw 1.460 2.230 nonbonded pdb=" OQ1 KCX H 210 " pdb="ZN ZN H 502 " model vdw 1.528 2.230 nonbonded pdb="ZN ZN G 502 " pdb=" OAX 97U G 503 " model vdw 1.769 2.230 nonbonded pdb="ZN ZN B 502 " pdb=" OAX 97U B 503 " model vdw 1.789 2.230 nonbonded pdb="ZN ZN A 502 " pdb=" OAX 97U A 503 " model vdw 1.825 2.230 ... (remaining 202595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.340 Find NCS groups from input model: 0.380 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:7.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.009 0.472 24888 Z= 0.356 Angle : 0.649 13.133 33736 Z= 0.339 Chirality : 0.047 0.364 3688 Planarity : 0.005 0.041 4488 Dihedral : 17.351 89.125 9096 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.37 % Allowed : 19.66 % Favored : 79.97 % 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: -0.23 (0.15), residues: 3136 helix: 0.67 (0.15), residues: 1256 sheet: -0.58 (0.25), residues: 448 loop : -0.66 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 315 TYR 0.011 0.001 TYR C 333 PHE 0.013 0.002 PHE H 294 TRP 0.004 0.001 TRP H 79 HIS 0.011 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00534 (24848) covalent geometry : angle 0.64733 (33720) SS BOND : bond 0.00852 ( 8) SS BOND : angle 2.37509 ( 16) hydrogen bonds : bond 0.16419 ( 983) hydrogen bonds : angle 5.09486 ( 2685) metal coordination : bond 0.18535 ( 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 466 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 457 time to evaluate : 0.988 Fit side-chains REVERT: E 44 LEU cc_start: 0.8128 (mp) cc_final: 0.7892 (mm) REVERT: E 172 GLU cc_start: 0.7459 (pt0) cc_final: 0.7085 (tt0) REVERT: E 174 LEU cc_start: 0.7722 (mt) cc_final: 0.7512 (mt) REVERT: E 281 ARG cc_start: 0.7358 (mtp180) cc_final: 0.7134 (mtm110) REVERT: E 327 GLN cc_start: 0.6857 (mp-120) cc_final: 0.6452 (mm-40) REVERT: F 44 LEU cc_start: 0.8116 (mp) cc_final: 0.7894 (mm) REVERT: F 155 LYS cc_start: 0.8035 (tptp) cc_final: 0.7828 (tptp) REVERT: F 172 GLU cc_start: 0.7454 (pt0) cc_final: 0.6935 (mm-30) REVERT: F 174 LEU cc_start: 0.7628 (mt) cc_final: 0.7409 (mt) REVERT: F 281 ARG cc_start: 0.7371 (mtp180) cc_final: 0.7145 (mtm110) REVERT: F 327 GLN cc_start: 0.6872 (mp-120) cc_final: 0.6475 (mm-40) REVERT: G 44 LEU cc_start: 0.8140 (mp) cc_final: 0.7901 (mm) REVERT: G 155 LYS cc_start: 0.8043 (tptp) cc_final: 0.7839 (tptp) REVERT: G 172 GLU cc_start: 0.7450 (pt0) cc_final: 0.7064 (tt0) REVERT: G 174 LEU cc_start: 0.7697 (mt) cc_final: 0.7480 (mt) REVERT: G 207 ASP cc_start: 0.8386 (m-30) cc_final: 0.8139 (m-30) REVERT: G 281 ARG cc_start: 0.7426 (mtp180) cc_final: 0.7191 (mtm110) REVERT: G 327 GLN cc_start: 0.6797 (mp-120) cc_final: 0.6399 (mm-40) REVERT: H 44 LEU cc_start: 0.8119 (mp) cc_final: 0.7873 (mm) REVERT: H 155 LYS cc_start: 0.8013 (tptp) cc_final: 0.7807 (tptp) REVERT: H 174 LEU cc_start: 0.7662 (mt) cc_final: 0.7458 (mt) REVERT: H 281 ARG cc_start: 0.7375 (mtp180) cc_final: 0.7146 (mtm110) REVERT: H 327 GLN cc_start: 0.6826 (mp-120) cc_final: 0.6437 (mm-40) outliers start: 9 outliers final: 9 residues processed: 465 average time/residue: 0.7918 time to fit residues: 415.2821 Evaluate side-chains 374 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 365 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain H residue 251 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0870 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 404 ASN B 26 GLN B 53 GLN B 404 ASN C 26 GLN C 53 GLN C 404 ASN D 26 GLN D 53 GLN D 404 ASN E 26 GLN E 53 GLN E 93 GLN E 404 ASN F 26 GLN F 53 GLN F 93 GLN F 404 ASN G 26 GLN G 53 GLN G 93 GLN G 404 ASN H 26 GLN H 53 GLN H 93 GLN H 404 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105390 restraints weight = 24672.214| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.64 r_work: 0.3138 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24888 Z= 0.179 Angle : 0.568 7.669 33736 Z= 0.305 Chirality : 0.047 0.229 3688 Planarity : 0.005 0.045 4488 Dihedral : 10.302 86.940 3771 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.15 % Allowed : 16.76 % Favored : 80.09 % 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: 0.84 (0.15), residues: 1264 sheet: 0.03 (0.25), residues: 472 loop : -0.79 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 137 TYR 0.014 0.002 TYR D 333 PHE 0.015 0.002 PHE E 294 TRP 0.008 0.001 TRP F 289 HIS 0.007 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00416 (24848) covalent geometry : angle 0.56766 (33720) SS BOND : bond 0.01166 ( 8) SS BOND : angle 0.90632 ( 16) hydrogen bonds : bond 0.05944 ( 983) hydrogen bonds : angle 3.87536 ( 2685) metal coordination : bond 0.00983 ( 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 429 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 353 time to evaluate : 1.024 Fit side-chains REVERT: A 52 ARG cc_start: 0.7309 (mtm180) cc_final: 0.6820 (mpt-90) REVERT: A 270 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8285 (mm-30) REVERT: B 270 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8268 (mm-30) REVERT: C 270 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8271 (mm-30) REVERT: D 270 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8277 (mm-30) REVERT: E 44 LEU cc_start: 0.8466 (mp) cc_final: 0.8151 (mm) REVERT: E 172 GLU cc_start: 0.7808 (pt0) cc_final: 0.7581 (pt0) REVERT: E 281 ARG cc_start: 0.7789 (mtp180) cc_final: 0.7388 (mtm110) REVERT: E 414 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7761 (t70) REVERT: F 44 LEU cc_start: 0.8472 (mp) cc_final: 0.8169 (mm) REVERT: F 131 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8077 (mt-10) REVERT: F 172 GLU cc_start: 0.7822 (pt0) cc_final: 0.7601 (pt0) REVERT: F 281 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7375 (mtm110) REVERT: F 414 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7770 (t70) REVERT: G 44 LEU cc_start: 0.8493 (mp) cc_final: 0.8184 (mm) REVERT: G 172 GLU cc_start: 0.7814 (pt0) cc_final: 0.7607 (pt0) REVERT: G 174 LEU cc_start: 0.7842 (mt) cc_final: 0.7588 (mt) REVERT: G 281 ARG cc_start: 0.7800 (mtp180) cc_final: 0.7405 (mtm110) REVERT: G 414 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7746 (t70) REVERT: H 44 LEU cc_start: 0.8486 (mp) cc_final: 0.8163 (mm) REVERT: H 281 ARG cc_start: 0.7786 (mtp180) cc_final: 0.7379 (mtm110) REVERT: H 414 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7759 (t70) outliers start: 76 outliers final: 33 residues processed: 402 average time/residue: 0.7644 time to fit residues: 348.8325 Evaluate side-chains 371 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 329 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 150 optimal weight: 6.9990 chunk 263 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 297 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN B 26 GLN B 53 GLN C 26 GLN C 53 GLN D 26 GLN D 53 GLN E 26 GLN E 53 GLN E 93 GLN F 53 GLN F 93 GLN G 26 GLN G 53 GLN G 93 GLN H 26 GLN H 53 GLN H 93 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104672 restraints weight = 24205.923| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.62 r_work: 0.3116 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 24888 Z= 0.225 Angle : 0.613 9.817 33736 Z= 0.329 Chirality : 0.049 0.228 3688 Planarity : 0.006 0.047 4488 Dihedral : 10.084 83.324 3771 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.14 % Allowed : 15.60 % Favored : 80.26 % 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: -0.20 (0.15), residues: 3136 helix: 0.73 (0.14), residues: 1264 sheet: 0.12 (0.27), residues: 432 loop : -0.96 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 247 TYR 0.015 0.002 TYR C 333 PHE 0.018 0.002 PHE H 294 TRP 0.009 0.002 TRP H 289 HIS 0.008 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00533 (24848) covalent geometry : angle 0.61330 (33720) SS BOND : bond 0.01163 ( 8) SS BOND : angle 0.91551 ( 16) hydrogen bonds : bond 0.06643 ( 983) hydrogen bonds : angle 3.83818 ( 2685) metal coordination : bond 0.00670 ( 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 441 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 341 time to evaluate : 0.886 Fit side-chains REVERT: A 52 ARG cc_start: 0.7391 (mtm180) cc_final: 0.6809 (mpt-90) REVERT: A 270 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8398 (mm-30) REVERT: B 270 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8369 (mm-30) REVERT: C 270 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8380 (mm-30) REVERT: D 270 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8377 (mm-30) REVERT: E 44 LEU cc_start: 0.8549 (mp) cc_final: 0.8245 (mm) REVERT: E 173 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.5993 (ttm170) REVERT: E 414 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7737 (t70) REVERT: F 44 LEU cc_start: 0.8546 (mp) cc_final: 0.8240 (mm) REVERT: F 131 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: F 173 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6112 (ttm170) REVERT: F 414 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7751 (t70) REVERT: G 44 LEU cc_start: 0.8552 (mp) cc_final: 0.8255 (mm) REVERT: G 173 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6031 (ttm170) REVERT: G 404 ASN cc_start: 0.8594 (t0) cc_final: 0.8387 (t0) REVERT: G 414 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7737 (t70) REVERT: H 44 LEU cc_start: 0.8546 (mp) cc_final: 0.8244 (mm) REVERT: H 173 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6081 (ttm170) REVERT: H 414 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7787 (t70) outliers start: 100 outliers final: 37 residues processed: 407 average time/residue: 0.7508 time to fit residues: 345.8993 Evaluate side-chains 383 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 333 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 289 optimal weight: 3.9990 chunk 265 optimal weight: 0.0980 chunk 275 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 304 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 232 optimal weight: 0.3980 chunk 164 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 255 optimal weight: 0.7980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 26 GLN B 53 GLN B 404 ASN C 26 GLN C 53 GLN C 404 ASN D 26 GLN D 53 GLN D 404 ASN E 53 GLN E 93 GLN E 404 ASN F 53 GLN F 93 GLN F 404 ASN G 53 GLN G 93 GLN H 53 GLN H 93 GLN H 404 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111089 restraints weight = 24346.426| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.60 r_work: 0.3216 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 24888 Z= 0.089 Angle : 0.440 5.053 33736 Z= 0.232 Chirality : 0.043 0.220 3688 Planarity : 0.004 0.043 4488 Dihedral : 7.741 70.066 3771 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.98 % Allowed : 16.18 % Favored : 80.84 % 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: 0.35 (0.15), residues: 3136 helix: 1.46 (0.15), residues: 1208 sheet: 0.26 (0.26), residues: 432 loop : -0.79 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 201 TYR 0.007 0.001 TYR B 333 PHE 0.011 0.001 PHE H 294 TRP 0.003 0.001 TRP E 289 HIS 0.002 0.000 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00186 (24848) covalent geometry : angle 0.43954 (33720) SS BOND : bond 0.00535 ( 8) SS BOND : angle 0.96525 ( 16) hydrogen bonds : bond 0.03486 ( 983) hydrogen bonds : angle 3.46768 ( 2685) metal coordination : bond 0.00093 ( 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 414 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 342 time to evaluate : 0.729 Fit side-chains REVERT: A 52 ARG cc_start: 0.7435 (mtm180) cc_final: 0.6896 (mpt-90) REVERT: A 173 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.5650 (ttm-80) REVERT: B 53 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: B 173 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.5662 (ttm-80) REVERT: C 53 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7735 (mt0) REVERT: C 173 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.5629 (ttm-80) REVERT: D 53 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7744 (mt0) REVERT: E 37 GLN cc_start: 0.6941 (mm-40) cc_final: 0.6154 (tt0) REVERT: E 173 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.5500 (ttm-80) REVERT: E 327 GLN cc_start: 0.6974 (mp10) cc_final: 0.6604 (mm-40) REVERT: E 362 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7618 (mt-10) REVERT: E 414 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7649 (t70) REVERT: F 37 GLN cc_start: 0.6963 (mm-40) cc_final: 0.6161 (tt0) REVERT: F 131 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: F 173 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6095 (ttm170) REVERT: F 327 GLN cc_start: 0.6975 (mp10) cc_final: 0.6608 (mm-40) REVERT: F 414 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7640 (t70) REVERT: G 173 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.5507 (ttm-80) REVERT: G 404 ASN cc_start: 0.8368 (t0) cc_final: 0.8141 (t0) REVERT: G 414 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7639 (t70) REVERT: H 173 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6097 (ttm170) REVERT: H 362 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7609 (mt-10) REVERT: H 414 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7648 (t70) outliers start: 72 outliers final: 26 residues processed: 382 average time/residue: 0.7073 time to fit residues: 307.6799 Evaluate side-chains 365 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 324 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 0.0000 chunk 1 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 237 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 239 optimal weight: 0.3980 chunk 198 optimal weight: 20.0000 chunk 199 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 overall best weight: 3.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 26 GLN C 26 GLN C 285 GLN D 26 GLN D 285 GLN E 26 GLN E 53 GLN E 404 ASN F 26 GLN F 53 GLN F 404 ASN G 26 GLN G 53 GLN H 26 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.105185 restraints weight = 24010.446| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.61 r_work: 0.3118 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 24888 Z= 0.220 Angle : 0.594 8.273 33736 Z= 0.320 Chirality : 0.049 0.220 3688 Planarity : 0.006 0.049 4488 Dihedral : 9.310 80.437 3752 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.64 % Allowed : 15.36 % Favored : 81.00 % 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: -0.02 (0.15), residues: 3136 helix: 0.91 (0.14), residues: 1264 sheet: 0.30 (0.25), residues: 472 loop : -0.95 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 247 TYR 0.015 0.002 TYR C 333 PHE 0.017 0.002 PHE H 294 TRP 0.008 0.002 TRP H 289 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00523 (24848) covalent geometry : angle 0.59345 (33720) SS BOND : bond 0.01134 ( 8) SS BOND : angle 1.06535 ( 16) hydrogen bonds : bond 0.06365 ( 983) hydrogen bonds : angle 3.70436 ( 2685) metal coordination : bond 0.00573 ( 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 421 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 333 time to evaluate : 0.965 Fit side-chains REVERT: A 52 ARG cc_start: 0.7431 (mtm180) cc_final: 0.6761 (mpt-90) REVERT: A 173 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.5701 (ttm-80) REVERT: B 173 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.5719 (ttm-80) REVERT: C 173 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.5729 (ttm-80) REVERT: E 37 GLN cc_start: 0.7105 (mm-40) cc_final: 0.6407 (tt0) REVERT: E 173 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6003 (ttm170) REVERT: E 414 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7709 (t70) REVERT: F 37 GLN cc_start: 0.7103 (mm-40) cc_final: 0.6405 (tt0) REVERT: F 131 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8103 (mt-10) REVERT: F 173 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6025 (ttm170) REVERT: F 414 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7727 (t70) REVERT: G 173 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.5989 (ttm170) REVERT: G 404 ASN cc_start: 0.8508 (t0) cc_final: 0.8286 (t0) REVERT: G 414 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7727 (t70) REVERT: H 37 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6213 (tt0) REVERT: H 173 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.5980 (ttm170) REVERT: H 414 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7751 (t70) outliers start: 88 outliers final: 40 residues processed: 397 average time/residue: 0.7201 time to fit residues: 325.4486 Evaluate side-chains 364 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 312 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 209 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 222 optimal weight: 0.0770 chunk 202 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 267 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 118 optimal weight: 0.0370 overall best weight: 1.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 404 ASN B 26 GLN B 53 GLN B 285 GLN B 404 ASN C 26 GLN C 53 GLN C 285 GLN C 404 ASN D 26 GLN D 53 GLN D 285 GLN E 26 GLN E 53 GLN E 404 ASN F 26 GLN F 53 GLN F 404 ASN G 26 GLN G 53 GLN H 26 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107998 restraints weight = 24037.607| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.61 r_work: 0.3159 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 24888 Z= 0.124 Angle : 0.490 6.522 33736 Z= 0.261 Chirality : 0.044 0.225 3688 Planarity : 0.005 0.042 4488 Dihedral : 8.414 77.800 3752 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.98 % Allowed : 15.65 % Favored : 81.37 % 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 (0.15), residues: 3136 helix: 1.10 (0.15), residues: 1264 sheet: 0.36 (0.25), residues: 472 loop : -0.87 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 315 TYR 0.010 0.001 TYR B 333 PHE 0.013 0.001 PHE G 294 TRP 0.005 0.001 TRP E 289 HIS 0.003 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00277 (24848) covalent geometry : angle 0.48944 (33720) SS BOND : bond 0.00671 ( 8) SS BOND : angle 1.00465 ( 16) hydrogen bonds : bond 0.04652 ( 983) hydrogen bonds : angle 3.53671 ( 2685) metal coordination : bond 0.00284 ( 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 396 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 324 time to evaluate : 0.925 Fit side-chains REVERT: A 52 ARG cc_start: 0.7432 (mtm180) cc_final: 0.6743 (mpt-90) REVERT: A 173 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.5730 (ttm-80) REVERT: B 173 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.5737 (ttm-80) REVERT: C 173 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.5731 (ttm-80) REVERT: E 173 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.5962 (ttm170) REVERT: E 414 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7698 (t70) REVERT: F 173 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6021 (ttm170) REVERT: F 414 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7679 (t70) REVERT: G 173 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.5996 (ttm170) REVERT: G 404 ASN cc_start: 0.8352 (t0) cc_final: 0.8151 (t0) REVERT: G 414 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7691 (t70) REVERT: H 173 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.5965 (ttm170) REVERT: H 414 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7712 (t70) outliers start: 72 outliers final: 39 residues processed: 375 average time/residue: 0.6745 time to fit residues: 289.5456 Evaluate side-chains 370 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 320 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 298 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 307 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 311 optimal weight: 5.9990 chunk 18 optimal weight: 0.0670 chunk 302 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 278 optimal weight: 4.9990 chunk 160 optimal weight: 0.0170 chunk 203 optimal weight: 4.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 26 GLN B 53 GLN B 285 GLN C 26 GLN C 53 GLN C 285 GLN D 26 GLN D 53 GLN D 285 GLN D 404 ASN E 53 GLN E 404 ASN F 53 GLN F 404 ASN G 53 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113090 restraints weight = 24120.344| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.62 r_work: 0.3231 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24888 Z= 0.082 Angle : 0.425 5.256 33736 Z= 0.223 Chirality : 0.043 0.212 3688 Planarity : 0.004 0.040 4488 Dihedral : 6.254 53.919 3752 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.36 % Allowed : 16.97 % Favored : 80.67 % 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: 0.55 (0.15), residues: 3136 helix: 1.71 (0.15), residues: 1208 sheet: 0.40 (0.26), residues: 432 loop : -0.77 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 52 TYR 0.006 0.001 TYR D 333 PHE 0.012 0.001 PHE F 294 TRP 0.003 0.001 TRP F 289 HIS 0.004 0.000 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00173 (24848) covalent geometry : angle 0.42457 (33720) SS BOND : bond 0.00440 ( 8) SS BOND : angle 0.98753 ( 16) hydrogen bonds : bond 0.03249 ( 983) hydrogen bonds : angle 3.35283 ( 2685) metal coordination : bond 0.00118 ( 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 377 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 320 time to evaluate : 0.950 Fit side-chains REVERT: A 52 ARG cc_start: 0.7508 (mtm180) cc_final: 0.6755 (mpt-90) REVERT: A 173 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.5663 (ttm-80) REVERT: A 313 VAL cc_start: 0.5895 (OUTLIER) cc_final: 0.5657 (p) REVERT: B 53 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: B 173 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.5662 (ttm-80) REVERT: B 313 VAL cc_start: 0.5903 (OUTLIER) cc_final: 0.5668 (p) REVERT: C 53 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7785 (mt0) REVERT: C 173 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.5640 (ttm-80) REVERT: C 313 VAL cc_start: 0.5887 (OUTLIER) cc_final: 0.5647 (p) REVERT: D 53 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: D 313 VAL cc_start: 0.5908 (OUTLIER) cc_final: 0.5672 (p) REVERT: E 207 ASP cc_start: 0.8535 (m-30) cc_final: 0.8332 (m-30) REVERT: E 327 GLN cc_start: 0.7005 (mp10) cc_final: 0.6606 (mm-40) REVERT: F 207 ASP cc_start: 0.8546 (m-30) cc_final: 0.8342 (m-30) REVERT: F 327 GLN cc_start: 0.7008 (mp10) cc_final: 0.6599 (mm-40) REVERT: G 327 GLN cc_start: 0.7003 (mp10) cc_final: 0.6624 (mm-40) REVERT: H 327 GLN cc_start: 0.6968 (mp10) cc_final: 0.6583 (mm-40) outliers start: 57 outliers final: 27 residues processed: 363 average time/residue: 0.7329 time to fit residues: 302.0051 Evaluate side-chains 341 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 304 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 292 optimal weight: 0.0770 chunk 242 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 267 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 404 ASN B 53 GLN B 285 GLN B 404 ASN C 53 GLN C 285 GLN C 404 ASN D 53 GLN D 285 GLN E 26 GLN E 53 GLN E 404 ASN F 26 GLN F 53 GLN F 404 ASN G 26 GLN G 53 GLN G 404 ASN H 26 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.104477 restraints weight = 24061.349| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.61 r_work: 0.3121 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 24888 Z= 0.218 Angle : 0.593 8.548 33736 Z= 0.318 Chirality : 0.049 0.223 3688 Planarity : 0.005 0.047 4488 Dihedral : 9.139 81.972 3752 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.73 % Allowed : 17.59 % Favored : 79.68 % 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: 0.13 (0.15), residues: 3136 helix: 1.08 (0.15), residues: 1264 sheet: 0.45 (0.25), residues: 472 loop : -0.94 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 315 TYR 0.015 0.002 TYR A 333 PHE 0.018 0.002 PHE H 294 TRP 0.007 0.002 TRP G 289 HIS 0.005 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00517 (24848) covalent geometry : angle 0.59266 (33720) SS BOND : bond 0.01050 ( 8) SS BOND : angle 1.11850 ( 16) hydrogen bonds : bond 0.06328 ( 983) hydrogen bonds : angle 3.67237 ( 2685) metal coordination : bond 0.00550 ( 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 385 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 319 time to evaluate : 0.778 Fit side-chains REVERT: A 52 ARG cc_start: 0.7549 (mtm180) cc_final: 0.6797 (mpt-90) REVERT: A 173 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.5726 (ttm-80) REVERT: B 173 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.5740 (ttm-80) REVERT: C 173 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.5762 (ttm-80) REVERT: F 313 VAL cc_start: 0.5636 (OUTLIER) cc_final: 0.5179 (p) REVERT: G 313 VAL cc_start: 0.5614 (OUTLIER) cc_final: 0.5159 (p) REVERT: H 313 VAL cc_start: 0.5612 (OUTLIER) cc_final: 0.5167 (p) outliers start: 66 outliers final: 44 residues processed: 371 average time/residue: 0.6536 time to fit residues: 278.0863 Evaluate side-chains 359 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 309 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 66 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 207 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 242 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 285 GLN B 26 GLN B 53 GLN B 285 GLN C 26 GLN C 53 GLN C 285 GLN D 26 GLN D 53 GLN D 285 GLN D 404 ASN E 26 GLN E 53 GLN E 404 ASN F 26 GLN F 53 GLN F 404 ASN G 26 GLN G 53 GLN G 404 ASN H 26 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108354 restraints weight = 24150.244| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.62 r_work: 0.3165 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24888 Z= 0.121 Angle : 0.486 6.506 33736 Z= 0.258 Chirality : 0.044 0.222 3688 Planarity : 0.005 0.044 4488 Dihedral : 7.930 72.748 3752 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.07 % Allowed : 17.80 % Favored : 80.13 % 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: 0.27 (0.15), residues: 3136 helix: 1.25 (0.15), residues: 1264 sheet: 0.43 (0.24), residues: 472 loop : -0.88 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 315 TYR 0.010 0.001 TYR D 333 PHE 0.013 0.001 PHE G 294 TRP 0.005 0.001 TRP F 289 HIS 0.003 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00272 (24848) covalent geometry : angle 0.48564 (33720) SS BOND : bond 0.00649 ( 8) SS BOND : angle 1.01139 ( 16) hydrogen bonds : bond 0.04521 ( 983) hydrogen bonds : angle 3.50726 ( 2685) metal coordination : bond 0.00256 ( 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 355 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 305 time to evaluate : 0.943 Fit side-chains REVERT: A 52 ARG cc_start: 0.7523 (mtm180) cc_final: 0.6779 (mpt-90) REVERT: A 173 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.5687 (ttm-80) REVERT: B 173 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.5683 (ttm-80) REVERT: C 173 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.5722 (ttm-80) outliers start: 50 outliers final: 35 residues processed: 339 average time/residue: 0.6336 time to fit residues: 245.8486 Evaluate side-chains 340 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 302 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 21 optimal weight: 6.9990 chunk 267 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 196 optimal weight: 10.0000 chunk 106 optimal weight: 0.2980 chunk 299 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 chunk 272 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 404 ASN B 26 GLN B 53 GLN B 285 GLN B 404 ASN C 26 GLN C 53 GLN C 285 GLN C 404 ASN D 26 GLN D 53 GLN D 285 GLN E 26 GLN E 53 GLN E 404 ASN F 26 GLN F 53 GLN G 26 GLN G 53 GLN G 404 ASN H 26 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106554 restraints weight = 24014.523| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.61 r_work: 0.3137 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24888 Z= 0.168 Angle : 0.536 7.245 33736 Z= 0.287 Chirality : 0.046 0.222 3688 Planarity : 0.005 0.047 4488 Dihedral : 8.596 77.538 3752 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.15 % Allowed : 17.67 % Favored : 80.17 % 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: 0.16 (0.15), residues: 3136 helix: 1.15 (0.15), residues: 1264 sheet: 0.41 (0.24), residues: 472 loop : -0.96 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 315 TYR 0.013 0.002 TYR C 333 PHE 0.015 0.002 PHE H 294 TRP 0.006 0.001 TRP F 289 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00391 (24848) covalent geometry : angle 0.53603 (33720) SS BOND : bond 0.00863 ( 8) SS BOND : angle 1.05201 ( 16) hydrogen bonds : bond 0.05483 ( 983) hydrogen bonds : angle 3.60081 ( 2685) metal coordination : bond 0.00413 ( 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 363 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 311 time to evaluate : 0.996 Fit side-chains REVERT: A 52 ARG cc_start: 0.7654 (mtm180) cc_final: 0.6792 (mpt-90) REVERT: A 173 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.5634 (ttm-80) REVERT: B 173 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.5675 (ttm-80) REVERT: C 173 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.5699 (ttm-80) REVERT: F 93 GLN cc_start: 0.7860 (pm20) cc_final: 0.7647 (pm20) REVERT: F 313 VAL cc_start: 0.5663 (OUTLIER) cc_final: 0.5195 (p) REVERT: G 93 GLN cc_start: 0.7850 (pm20) cc_final: 0.7637 (pm20) REVERT: G 313 VAL cc_start: 0.5631 (OUTLIER) cc_final: 0.5168 (p) REVERT: H 313 VAL cc_start: 0.5612 (OUTLIER) cc_final: 0.5161 (p) outliers start: 52 outliers final: 36 residues processed: 350 average time/residue: 0.6541 time to fit residues: 262.4520 Evaluate side-chains 349 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 307 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 216 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 26 GLN B 53 GLN B 285 GLN C 26 GLN C 53 GLN C 285 GLN D 26 GLN D 53 GLN D 285 GLN E 26 GLN F 26 GLN F 404 ASN G 26 GLN G 53 GLN H 26 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.104755 restraints weight = 24160.215| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.61 r_work: 0.3125 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 24888 Z= 0.202 Angle : 0.577 8.944 33736 Z= 0.309 Chirality : 0.048 0.225 3688 Planarity : 0.005 0.048 4488 Dihedral : 9.276 79.465 3752 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.57 % Allowed : 17.43 % Favored : 80.01 % 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: 0.05 (0.15), residues: 3136 helix: 1.05 (0.15), residues: 1264 sheet: 0.40 (0.25), residues: 472 loop : -1.03 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 315 TYR 0.014 0.002 TYR D 333 PHE 0.016 0.002 PHE H 294 TRP 0.007 0.001 TRP F 289 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00477 (24848) covalent geometry : angle 0.57631 (33720) SS BOND : bond 0.00997 ( 8) SS BOND : angle 1.11823 ( 16) hydrogen bonds : bond 0.06075 ( 983) hydrogen bonds : angle 3.66111 ( 2685) metal coordination : bond 0.00518 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10050.27 seconds wall clock time: 171 minutes 14.04 seconds (10274.04 seconds total)