Starting phenix.real_space_refine on Mon Aug 25 00:39:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihq_35452/08_2025/8ihq_35452.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihq_35452/08_2025/8ihq_35452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihq_35452/08_2025/8ihq_35452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihq_35452/08_2025/8ihq_35452.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihq_35452/08_2025/8ihq_35452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihq_35452/08_2025/8ihq_35452.cif" } resolution = 2.71 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= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 16 6.06 5 S 72 5.16 5 C 15112 2.51 5 N 4416 2.21 5 O 4512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24128 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.75, per 1000 atoms: 0.24 Number of scatterers: 24128 At special positions: 0 Unit cell: (131.75, 131.75, 104.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 16 29.99 S 72 16.00 O 4512 8.00 N 4416 7.00 C 15112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 75 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 990.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 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 85 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 83 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 251 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 271 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 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 83 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 85 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 251 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 271 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 83 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 85 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 251 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 271 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 83 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 85 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 271 " pdb="ZN ZN G 502 " - pdb=" ND1 HIS G 251 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 83 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 85 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" ND1 HIS H 251 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 271 " 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5664 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 24 sheets defined 40.5% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 93 through 97 removed outlier: 3.515A pdb=" N SER A 96 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.525A pdb=" N HIS A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.161A 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 190 through 204 removed outlier: 3.538A pdb=" N ARG A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 245 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.681A pdb=" N GLY A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 354 through 362 removed outlier: 4.051A pdb=" N VAL A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.759A pdb=" N ALA A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.901A pdb=" N ALA A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 102 through 120 removed outlier: 3.544A pdb=" N HIS B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 115 " --> pdb=" O VAL B 111 " (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 190 through 204 Processing helix chain 'B' and resid 230 through 244 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 305 removed outlier: 3.538A pdb=" N GLY B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 354 through 362 removed outlier: 3.972A pdb=" N VAL B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 374 removed outlier: 3.762A pdb=" N ALA B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.903A pdb=" N ALA B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 removed outlier: 3.541A pdb=" N ALA B 411 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 102 through 120 removed outlier: 3.550A pdb=" N HIS C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 120 " --> pdb=" O LYS C 116 " (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 190 through 204 Processing helix chain 'C' and resid 230 through 244 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 305 removed outlier: 3.537A pdb=" N GLY C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 322 Processing helix chain 'C' and resid 325 through 336 Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.977A pdb=" N VAL C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 374 removed outlier: 3.761A pdb=" N ALA C 374 " --> pdb=" O ALA C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 383 removed outlier: 3.903A pdb=" N ALA C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN C 380 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'D' and resid 93 through 97 Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.544A pdb=" N HIS D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 120 " --> pdb=" O LYS D 116 " (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 190 through 204 Processing helix chain 'D' and resid 230 through 244 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 305 removed outlier: 3.538A pdb=" N GLY D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 322 Processing helix chain 'D' and resid 325 through 336 Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.972A pdb=" N VAL D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 374 removed outlier: 3.762A pdb=" N ALA D 374 " --> pdb=" O ALA D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 383 removed outlier: 3.903A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN D 380 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 removed outlier: 3.598A pdb=" N ALA D 411 " --> pdb=" O ASP D 408 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 412 " --> pdb=" O ILE D 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 removed outlier: 4.146A 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 177 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.504A pdb=" N ASP E 243 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 3.645A 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 305 removed outlier: 3.716A pdb=" N GLY E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 322 removed outlier: 3.761A pdb=" N GLY E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 335 Processing helix chain 'E' and resid 354 through 362 removed outlier: 4.027A 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 removed outlier: 3.718A pdb=" N ALA E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN E 380 " --> pdb=" O VAL E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 413 removed outlier: 3.872A pdb=" N VAL E 412 " --> pdb=" O ILE E 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 120 removed outlier: 4.146A 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 190 through 204 Processing helix chain 'F' and resid 230 through 244 removed outlier: 3.502A pdb=" N ASP F 243 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 3.649A 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 305 removed outlier: 3.715A pdb=" N GLY F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA F 305 " --> pdb=" O THR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 322 removed outlier: 3.791A pdb=" N GLY F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 335 Processing helix chain 'F' and resid 354 through 362 removed outlier: 4.026A 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 removed outlier: 3.723A pdb=" N ALA F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN F 380 " --> pdb=" O VAL F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 413 removed outlier: 3.870A pdb=" N VAL F 412 " --> pdb=" O ILE F 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 120 removed outlier: 4.146A 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 190 through 204 Processing helix chain 'G' and resid 230 through 244 removed outlier: 3.651A pdb=" N TYR G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 265 Processing helix chain 'G' and resid 276 through 287 Processing helix chain 'G' and resid 293 through 304 removed outlier: 3.715A pdb=" N GLY G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 322 removed outlier: 3.804A pdb=" N GLY G 322 " --> pdb=" O ALA G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 335 Processing helix chain 'G' and resid 354 through 362 removed outlier: 4.026A 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 removed outlier: 3.728A pdb=" N ALA G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN G 380 " --> pdb=" O VAL G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 413 removed outlier: 3.874A pdb=" N VAL G 412 " --> pdb=" O ILE G 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 120 removed outlier: 4.148A 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 190 through 204 Processing helix chain 'H' and resid 230 through 244 removed outlier: 3.651A 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 305 removed outlier: 3.717A pdb=" N GLY H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA H 305 " --> pdb=" O THR H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 322 removed outlier: 3.801A pdb=" N GLY H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 335 Processing helix chain 'H' and resid 354 through 362 removed outlier: 4.028A 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 removed outlier: 3.724A pdb=" N ALA H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN H 380 " --> pdb=" O VAL H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 413 removed outlier: 3.875A pdb=" N VAL H 412 " --> pdb=" O ILE H 409 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 56 removed outlier: 6.570A pdb=" N LEU A 45 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 54 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR A 43 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 13.640A pdb=" N VAL A 23 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 14.176A pdb=" N GLY A 71 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 12.618A pdb=" N VAL A 25 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 11.086A pdb=" N LYS A 73 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS A 27 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N CYS A 75 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG A 29 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL A 418 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 84 removed outlier: 6.390A pdb=" N TRP A 79 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ARG A 126 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP A 81 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 212 removed outlier: 6.546A pdb=" N ILE A 209 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N HIS A 251 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE A 211 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 268 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 56 removed outlier: 6.576A pdb=" N LEU B 45 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL B 54 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR B 43 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 13.640A pdb=" N VAL B 23 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 14.169A pdb=" N GLY B 71 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 12.620A pdb=" N VAL B 25 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 11.086A pdb=" N LYS B 73 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS B 27 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N CYS B 75 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG B 29 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL B 418 " --> pdb=" O TYR B 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 84 removed outlier: 6.388A pdb=" N TRP B 79 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ARG B 126 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASP B 81 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.540A pdb=" N ILE B 209 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS B 251 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE B 211 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 268 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 56 removed outlier: 6.569A pdb=" N LEU C 45 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL C 54 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR C 43 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 13.640A pdb=" N VAL C 23 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 14.180A pdb=" N GLY C 71 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 12.619A pdb=" N VAL C 25 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N LYS C 73 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS C 27 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N CYS C 75 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG C 29 " --> pdb=" O CYS C 75 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL C 418 " --> pdb=" O TYR C 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 79 through 84 removed outlier: 6.388A pdb=" N TRP C 79 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ARG C 126 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASP C 81 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 209 through 212 removed outlier: 6.531A pdb=" N ILE C 209 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N HIS C 251 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE C 211 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 268 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 50 through 56 removed outlier: 6.576A pdb=" N LEU D 45 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL D 54 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR D 43 " --> pdb=" O VAL D 54 " (cutoff:3.500A) removed outlier: 13.791A pdb=" N VAL D 23 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 13.994A pdb=" N GLY D 71 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 12.382A pdb=" N VAL D 25 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N LYS D 73 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N CYS D 27 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N CYS D 75 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG D 29 " --> pdb=" O CYS D 75 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL D 418 " --> pdb=" O TYR D 425 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.389A pdb=" N TRP D 79 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ARG D 126 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP D 81 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 209 through 212 removed outlier: 6.555A pdb=" N ILE D 209 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS D 251 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE D 211 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER D 268 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 50 through 56 removed outlier: 6.588A pdb=" N LEU E 45 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL E 54 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR E 43 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 13.514A pdb=" N VAL E 23 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 13.810A pdb=" N GLY E 71 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 12.702A pdb=" N VAL E 25 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 11.176A pdb=" N LYS E 73 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N CYS E 27 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N CYS E 75 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG E 29 " --> pdb=" O CYS E 75 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL E 398 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL E 418 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA E 400 " --> pdb=" O ARG E 416 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS E 426 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS E 420 " --> pdb=" O ILE E 424 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE E 424 " --> pdb=" O LYS E 420 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 79 through 84 removed outlier: 6.321A pdb=" N TRP E 79 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ARG E 126 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP E 81 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 156 through 157 removed outlier: 6.684A pdb=" N ILE E 209 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N HIS E 251 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE E 211 " --> pdb=" O HIS E 251 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER E 268 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 50 through 56 removed outlier: 6.587A pdb=" N LEU F 45 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL F 54 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR F 43 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA F 24 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU F 70 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLN F 26 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP F 72 " --> pdb=" O GLN F 26 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLY F 28 " --> pdb=" O ASP F 72 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL F 74 " --> pdb=" O GLY F 28 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU F 30 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU F 76 " --> pdb=" O LEU F 30 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL F 398 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL F 418 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA F 400 " --> pdb=" O ARG F 416 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS F 426 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS F 420 " --> pdb=" O ILE F 424 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 79 through 84 removed outlier: 6.303A pdb=" N TRP F 79 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ARG F 126 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP F 81 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 156 through 157 removed outlier: 6.683A pdb=" N ILE F 209 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N HIS F 251 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE F 211 " --> pdb=" O HIS F 251 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER F 268 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 50 through 56 removed outlier: 6.609A pdb=" N LEU G 45 " --> pdb=" O ARG G 52 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL G 54 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR G 43 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 13.506A pdb=" N VAL G 23 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 13.814A pdb=" N GLY G 71 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N VAL G 25 " --> pdb=" O GLY G 71 " (cutoff:3.500A) removed outlier: 11.189A pdb=" N LYS G 73 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N CYS G 27 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N CYS G 75 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG G 29 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL G 398 " --> pdb=" O VAL G 418 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL G 418 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA G 400 " --> pdb=" O ARG G 416 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS G 426 " --> pdb=" O VAL G 418 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS G 420 " --> pdb=" O ILE G 424 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE G 424 " --> pdb=" O LYS G 420 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 79 through 84 removed outlier: 6.325A pdb=" N TRP G 79 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ARG G 126 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASP G 81 " --> pdb=" O ARG G 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 156 through 157 removed outlier: 6.684A pdb=" N ILE G 209 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N HIS G 251 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE G 211 " --> pdb=" O HIS G 251 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER G 268 " --> pdb=" O VAL G 248 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 50 through 56 removed outlier: 6.584A pdb=" N LEU H 45 " --> pdb=" O ARG H 52 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL H 54 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR H 43 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA H 24 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU H 70 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN H 26 " --> pdb=" O LEU H 70 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP H 72 " --> pdb=" O GLN H 26 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLY H 28 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL H 74 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU H 30 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU H 76 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL H 398 " --> pdb=" O VAL H 418 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL H 418 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA H 400 " --> pdb=" O ARG H 416 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS H 426 " --> pdb=" O VAL H 418 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS H 420 " --> pdb=" O ILE H 424 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE H 424 " --> pdb=" O LYS H 420 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 79 through 84 removed outlier: 6.322A pdb=" N TRP H 79 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ARG H 126 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP H 81 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 156 through 157 removed outlier: 6.684A pdb=" N ILE H 209 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N HIS H 251 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE H 211 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER H 268 " --> pdb=" O VAL H 248 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2670 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: 3.92 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5989 1.33 - 1.45: 4852 1.45 - 1.57: 13639 1.57 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 24608 Sorted by residual: bond pdb=" NZ KCX E 210 " pdb=" CX KCX E 210 " ideal model delta sigma weight residual 1.411 1.326 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" NZ KCX F 210 " pdb=" CX KCX F 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX H 210 " pdb=" CX KCX H 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX G 210 " pdb=" CX KCX G 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" NZ KCX D 210 " pdb=" CX KCX D 210 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 24603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 32322 1.42 - 2.84: 831 2.84 - 4.26: 162 4.26 - 5.68: 38 5.68 - 7.10: 23 Bond angle restraints: 33376 Sorted by residual: angle pdb=" CA GLY G 179 " pdb=" C GLY G 179 " pdb=" O GLY G 179 " ideal model delta sigma weight residual 122.29 118.22 4.07 8.10e-01 1.52e+00 2.53e+01 angle pdb=" CA GLY E 179 " pdb=" C GLY E 179 " pdb=" O GLY E 179 " ideal model delta sigma weight residual 122.39 118.05 4.34 9.30e-01 1.16e+00 2.18e+01 angle pdb=" N VAL G 178 " pdb=" CA VAL G 178 " pdb=" C VAL G 178 " ideal model delta sigma weight residual 112.96 108.52 4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" CA THR H 230 " pdb=" C THR H 230 " pdb=" O THR H 230 " ideal model delta sigma weight residual 121.72 117.39 4.33 1.18e+00 7.18e-01 1.35e+01 angle pdb=" CA GLY D 215 " pdb=" C GLY D 215 " pdb=" O GLY D 215 " ideal model delta sigma weight residual 122.75 118.27 4.48 1.27e+00 6.20e-01 1.25e+01 ... (remaining 33371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 12701 17.64 - 35.28: 1360 35.28 - 52.91: 377 52.91 - 70.55: 113 70.55 - 88.19: 25 Dihedral angle restraints: 14576 sinusoidal: 5632 harmonic: 8944 Sorted by residual: dihedral pdb=" CB CYS H 27 " pdb=" SG CYS H 27 " pdb=" SG CYS H 75 " pdb=" CB CYS H 75 " ideal model delta sinusoidal sigma weight residual -86.00 -123.29 37.29 1 1.00e+01 1.00e-02 1.96e+01 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 -86.00 -123.17 37.17 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CA GLY E 346 " pdb=" C GLY E 346 " pdb=" N VAL E 347 " pdb=" CA VAL E 347 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 14573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2827 0.050 - 0.100: 645 0.100 - 0.151: 186 0.151 - 0.201: 12 0.201 - 0.251: 2 Chirality restraints: 3672 Sorted by residual: chirality pdb=" CA VAL C 188 " pdb=" N VAL C 188 " pdb=" C VAL C 188 " pdb=" CB VAL C 188 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU D 70 " pdb=" N LEU D 70 " pdb=" C LEU D 70 " pdb=" CB LEU D 70 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL D 188 " pdb=" N VAL D 188 " pdb=" C VAL D 188 " pdb=" CB VAL D 188 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.37e-01 ... (remaining 3669 not shown) Planarity restraints: 4448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 55 " -0.054 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO D 56 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO D 56 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 56 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 55 " 0.053 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO C 56 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 56 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 56 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 55 " 0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO B 56 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 56 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 56 " 0.044 5.00e-02 4.00e+02 ... (remaining 4445 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 266 2.66 - 3.22: 20642 3.22 - 3.78: 35742 3.78 - 4.34: 54571 4.34 - 4.90: 89529 Nonbonded interactions: 200750 Sorted by model distance: nonbonded pdb=" OQ1 KCX C 210 " pdb="ZN ZN C 501 " model vdw 2.095 2.230 nonbonded pdb=" OQ1 KCX A 210 " pdb="ZN ZN A 501 " model vdw 2.095 2.230 nonbonded pdb=" OQ1 KCX B 210 " pdb="ZN ZN B 501 " model vdw 2.096 2.230 nonbonded pdb=" OQ1 KCX D 210 " pdb="ZN ZN D 501 " model vdw 2.097 2.230 nonbonded pdb=" NZ LYS D 155 " pdb=" O SER D 156 " model vdw 2.243 3.120 ... (remaining 200745 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: 0.02 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: 4.020 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: 0.250 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.880 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 : 0.005 0.195 24648 Z= 0.257 Angle : 0.586 7.097 33392 Z= 0.356 Chirality : 0.046 0.251 3672 Planarity : 0.005 0.082 4448 Dihedral : 16.578 88.189 8888 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.62 % Allowed : 18.96 % Favored : 80.42 % 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: -0.68 (0.14), residues: 3136 helix: 0.01 (0.14), residues: 1320 sheet: 0.35 (0.25), residues: 384 loop : -1.04 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 281 TYR 0.009 0.001 TYR C 333 PHE 0.011 0.001 PHE F 294 TRP 0.006 0.001 TRP E 289 HIS 0.007 0.001 HIS E 251 Details of bonding type rmsd covalent geometry : bond 0.00386 (24608) covalent geometry : angle 0.58598 (33376) SS BOND : bond 0.00260 ( 8) SS BOND : angle 0.48349 ( 16) hydrogen bonds : bond 0.16082 ( 953) hydrogen bonds : angle 5.18241 ( 2670) metal coordination : bond 0.06741 ( 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 348 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 333 time to evaluate : 0.805 Fit side-chains REVERT: B 281 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7310 (ttp-110) REVERT: C 331 LYS cc_start: 0.7476 (tttp) cc_final: 0.7252 (ttpp) REVERT: D 281 ARG cc_start: 0.7667 (mtm110) cc_final: 0.7245 (ttp-110) REVERT: E 98 ASP cc_start: 0.8069 (t0) cc_final: 0.7609 (m-30) REVERT: E 131 GLU cc_start: 0.7465 (mp0) cc_final: 0.7239 (mp0) REVERT: E 397 ASP cc_start: 0.8441 (m-30) cc_final: 0.8116 (m-30) REVERT: F 98 ASP cc_start: 0.8085 (t0) cc_final: 0.7615 (m-30) REVERT: F 385 ASP cc_start: 0.7668 (p0) cc_final: 0.7109 (t0) REVERT: F 397 ASP cc_start: 0.8419 (m-30) cc_final: 0.8112 (m-30) REVERT: G 26 GLN cc_start: 0.8018 (mt0) cc_final: 0.7731 (mt0) REVERT: G 98 ASP cc_start: 0.8075 (t0) cc_final: 0.7605 (m-30) REVERT: G 335 ASN cc_start: 0.7684 (m-40) cc_final: 0.7352 (m110) REVERT: G 385 ASP cc_start: 0.7720 (p0) cc_final: 0.7187 (t0) REVERT: G 397 ASP cc_start: 0.8462 (m-30) cc_final: 0.8114 (m-30) REVERT: H 26 GLN cc_start: 0.8005 (mt0) cc_final: 0.7736 (mt0) REVERT: H 98 ASP cc_start: 0.8071 (t0) cc_final: 0.7599 (m-30) REVERT: H 385 ASP cc_start: 0.7701 (p0) cc_final: 0.7167 (t0) REVERT: H 397 ASP cc_start: 0.8429 (m-30) cc_final: 0.8122 (m-30) outliers start: 15 outliers final: 9 residues processed: 346 average time/residue: 0.6851 time to fit residues: 267.1453 Evaluate side-chains 326 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 317 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 231 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN C 285 GLN D 285 GLN E 53 GLN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.115830 restraints weight = 25066.281| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.55 r_work: 0.3192 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24648 Z= 0.118 Angle : 0.475 6.934 33392 Z= 0.252 Chirality : 0.044 0.127 3672 Planarity : 0.005 0.063 4448 Dihedral : 5.213 51.714 3558 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.44 % Allowed : 17.14 % Favored : 80.42 % 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: -0.22 (0.14), residues: 3136 helix: 0.56 (0.14), residues: 1320 sheet: 0.61 (0.25), residues: 384 loop : -1.00 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 281 TYR 0.010 0.001 TYR C 333 PHE 0.012 0.001 PHE H 294 TRP 0.006 0.001 TRP E 289 HIS 0.006 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00270 (24608) covalent geometry : angle 0.47465 (33376) SS BOND : bond 0.00249 ( 8) SS BOND : angle 0.52939 ( 16) hydrogen bonds : bond 0.04626 ( 953) hydrogen bonds : angle 3.75697 ( 2670) metal coordination : bond 0.00275 ( 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 369 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 310 time to evaluate : 1.028 Fit side-chains REVERT: A 50 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6442 (mtt90) REVERT: A 155 LYS cc_start: 0.7883 (tptp) cc_final: 0.7401 (tptp) REVERT: B 50 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6429 (mtt90) REVERT: B 155 LYS cc_start: 0.7866 (tptp) cc_final: 0.7394 (tptp) REVERT: C 50 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.5594 (mtt90) REVERT: C 155 LYS cc_start: 0.7853 (tptp) cc_final: 0.7374 (tptp) REVERT: D 50 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6413 (mtt90) REVERT: D 155 LYS cc_start: 0.7863 (tptp) cc_final: 0.7355 (tptp) REVERT: E 98 ASP cc_start: 0.8238 (t0) cc_final: 0.7989 (t0) REVERT: E 302 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: E 356 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6302 (tp30) REVERT: E 397 ASP cc_start: 0.8511 (m-30) cc_final: 0.8305 (m-30) REVERT: F 53 GLN cc_start: 0.8375 (pt0) cc_final: 0.7998 (mt0) REVERT: F 98 ASP cc_start: 0.8254 (t0) cc_final: 0.8015 (t0) REVERT: F 173 ARG cc_start: 0.7922 (tmm-80) cc_final: 0.7507 (ttt180) REVERT: F 235 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8118 (mttm) REVERT: F 302 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: F 356 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6305 (tp30) REVERT: F 385 ASP cc_start: 0.7802 (p0) cc_final: 0.7227 (t0) REVERT: G 98 ASP cc_start: 0.8241 (t0) cc_final: 0.7994 (t0) REVERT: G 302 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: G 356 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6310 (tp30) REVERT: G 385 ASP cc_start: 0.7789 (p0) cc_final: 0.7231 (t0) REVERT: H 98 ASP cc_start: 0.8258 (t0) cc_final: 0.8028 (t0) REVERT: H 302 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: H 356 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6322 (tp30) REVERT: H 385 ASP cc_start: 0.7782 (p0) cc_final: 0.7226 (t0) outliers start: 59 outliers final: 28 residues processed: 345 average time/residue: 0.7423 time to fit residues: 287.6334 Evaluate side-chains 336 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 295 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 15 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 284 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 278 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN C 285 GLN D 285 GLN E 42 HIS ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS G 176 HIS H 42 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.133463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.109376 restraints weight = 25433.287| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.55 r_work: 0.3125 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 24648 Z= 0.329 Angle : 0.687 8.379 33392 Z= 0.373 Chirality : 0.054 0.158 3672 Planarity : 0.006 0.056 4448 Dihedral : 5.875 54.487 3545 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.85 % Allowed : 16.31 % Favored : 79.84 % 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: -0.75 (0.14), residues: 3136 helix: 0.12 (0.14), residues: 1304 sheet: 1.22 (0.31), residues: 248 loop : -1.31 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 281 TYR 0.015 0.003 TYR C 333 PHE 0.020 0.003 PHE H 294 TRP 0.011 0.002 TRP F 289 HIS 0.006 0.002 HIS H 350 Details of bonding type rmsd covalent geometry : bond 0.00809 (24608) covalent geometry : angle 0.68712 (33376) SS BOND : bond 0.00312 ( 8) SS BOND : angle 1.01222 ( 16) hydrogen bonds : bond 0.07781 ( 953) hydrogen bonds : angle 4.18423 ( 2670) metal coordination : bond 0.00957 ( 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 386 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 293 time to evaluate : 0.798 Fit side-chains REVERT: A 50 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.5741 (mtt90) REVERT: A 116 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7664 (mtpt) REVERT: A 172 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7510 (pt0) REVERT: B 50 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.5744 (mtt90) REVERT: B 172 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7522 (pt0) REVERT: C 50 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.5725 (mtt90) REVERT: C 116 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8047 (mtpt) REVERT: C 172 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7494 (pt0) REVERT: C 222 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8293 (ttt180) REVERT: D 50 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.5741 (mtt90) REVERT: E 98 ASP cc_start: 0.8261 (t0) cc_final: 0.7679 (m-30) REVERT: E 331 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7747 (ttmm) REVERT: E 356 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6417 (tt0) REVERT: F 52 ARG cc_start: 0.7601 (mmt180) cc_final: 0.7321 (mmt180) REVERT: F 98 ASP cc_start: 0.8276 (t0) cc_final: 0.7674 (m-30) REVERT: F 155 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7537 (mptm) REVERT: F 173 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7397 (tmm-80) REVERT: F 356 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6461 (tt0) REVERT: G 52 ARG cc_start: 0.7467 (mmt180) cc_final: 0.7169 (mmt180) REVERT: G 98 ASP cc_start: 0.8258 (t0) cc_final: 0.7662 (m-30) REVERT: G 155 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7547 (mptm) REVERT: G 356 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6451 (tt0) REVERT: H 52 ARG cc_start: 0.7499 (mmt180) cc_final: 0.7293 (mmt180) REVERT: H 98 ASP cc_start: 0.8271 (t0) cc_final: 0.7675 (m-30) REVERT: H 356 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6418 (tt0) outliers start: 93 outliers final: 38 residues processed: 351 average time/residue: 0.6671 time to fit residues: 264.5799 Evaluate side-chains 339 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 283 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 203 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 311 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 264 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN B 404 ASN C 285 GLN C 404 ASN D 285 GLN D 404 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113994 restraints weight = 25056.635| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.58 r_work: 0.3195 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24648 Z= 0.131 Angle : 0.496 7.682 33392 Z= 0.262 Chirality : 0.044 0.131 3672 Planarity : 0.005 0.049 4448 Dihedral : 5.258 53.837 3545 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.98 % Allowed : 17.14 % Favored : 79.88 % 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: -0.34 (0.14), residues: 3136 helix: 0.52 (0.14), residues: 1312 sheet: 1.45 (0.31), residues: 248 loop : -1.16 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 281 TYR 0.010 0.001 TYR C 333 PHE 0.013 0.001 PHE H 294 TRP 0.007 0.001 TRP G 289 HIS 0.006 0.001 HIS H 251 Details of bonding type rmsd covalent geometry : bond 0.00304 (24608) covalent geometry : angle 0.49541 (33376) SS BOND : bond 0.00331 ( 8) SS BOND : angle 0.71386 ( 16) hydrogen bonds : bond 0.04710 ( 953) hydrogen bonds : angle 3.73083 ( 2670) metal coordination : bond 0.00339 ( 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 362 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 290 time to evaluate : 0.913 Fit side-chains REVERT: A 39 LYS cc_start: 0.8103 (mmtm) cc_final: 0.7579 (mtmt) REVERT: A 50 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6344 (mtt90) REVERT: A 116 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7351 (mtpt) REVERT: B 39 LYS cc_start: 0.8133 (mmtm) cc_final: 0.7607 (mtmt) REVERT: B 50 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6374 (mtt90) REVERT: B 52 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7583 (mtm110) REVERT: C 39 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7591 (mtmt) REVERT: C 50 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6308 (mtt90) REVERT: D 39 LYS cc_start: 0.8114 (mmtm) cc_final: 0.7597 (mtmt) REVERT: D 50 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.6368 (mtt90) REVERT: D 222 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8052 (ttt180) REVERT: E 98 ASP cc_start: 0.8215 (t0) cc_final: 0.7563 (m-30) REVERT: E 302 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6563 (mt-10) REVERT: E 356 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6282 (tp30) REVERT: F 98 ASP cc_start: 0.8216 (t0) cc_final: 0.7552 (m-30) REVERT: F 173 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7358 (tmm-80) REVERT: F 302 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6561 (mt-10) REVERT: F 356 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6281 (tp30) REVERT: F 385 ASP cc_start: 0.7810 (p0) cc_final: 0.7570 (p0) REVERT: G 52 ARG cc_start: 0.7409 (mmt180) cc_final: 0.7134 (mmt180) REVERT: G 98 ASP cc_start: 0.8222 (t0) cc_final: 0.7562 (m-30) REVERT: G 302 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6619 (mt-10) REVERT: G 356 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6262 (tp30) REVERT: G 385 ASP cc_start: 0.7816 (p0) cc_final: 0.7600 (p0) REVERT: H 52 ARG cc_start: 0.7453 (mmt180) cc_final: 0.7195 (mmt180) REVERT: H 98 ASP cc_start: 0.8235 (t0) cc_final: 0.7574 (m-30) REVERT: H 302 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6553 (mt-10) REVERT: H 356 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6275 (tp30) REVERT: H 385 ASP cc_start: 0.7815 (p0) cc_final: 0.7605 (p0) outliers start: 72 outliers final: 44 residues processed: 338 average time/residue: 0.6702 time to fit residues: 255.7748 Evaluate side-chains 343 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 284 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 398 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 305 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 chunk 187 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 253 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN B 404 ASN C 285 GLN C 404 ASN D 285 GLN D 404 ASN E 42 HIS ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111946 restraints weight = 25057.568| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.57 r_work: 0.3163 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 24648 Z= 0.191 Angle : 0.550 8.093 33392 Z= 0.295 Chirality : 0.047 0.136 3672 Planarity : 0.005 0.050 4448 Dihedral : 5.497 52.689 3545 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.44 % Allowed : 16.97 % Favored : 79.59 % 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: -0.44 (0.14), residues: 3136 helix: 0.50 (0.14), residues: 1304 sheet: 1.37 (0.31), residues: 248 loop : -1.26 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 281 TYR 0.012 0.002 TYR B 333 PHE 0.016 0.002 PHE F 294 TRP 0.008 0.001 TRP H 289 HIS 0.007 0.001 HIS F 271 Details of bonding type rmsd covalent geometry : bond 0.00462 (24608) covalent geometry : angle 0.55032 (33376) SS BOND : bond 0.00314 ( 8) SS BOND : angle 0.80537 ( 16) hydrogen bonds : bond 0.05808 ( 953) hydrogen bonds : angle 3.85931 ( 2670) metal coordination : bond 0.00540 ( 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 387 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 304 time to evaluate : 0.709 Fit side-chains REVERT: A 50 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6374 (mtt90) REVERT: A 116 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7581 (mtpt) REVERT: A 356 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: B 50 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6419 (mtt90) REVERT: B 52 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7618 (mtm110) REVERT: C 50 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6384 (mtt90) REVERT: C 116 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7968 (mtpt) REVERT: C 222 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8066 (ttt180) REVERT: D 50 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6394 (mtt90) REVERT: D 172 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7375 (pt0) REVERT: D 222 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8259 (ttt180) REVERT: E 52 ARG cc_start: 0.7436 (mmt180) cc_final: 0.7194 (mmt180) REVERT: E 98 ASP cc_start: 0.8202 (t0) cc_final: 0.7592 (m-30) REVERT: E 173 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7496 (tmm-80) REVERT: E 356 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6321 (tp30) REVERT: F 52 ARG cc_start: 0.7504 (mmt180) cc_final: 0.7144 (mmt180) REVERT: F 98 ASP cc_start: 0.8212 (t0) cc_final: 0.7589 (m-30) REVERT: F 173 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7379 (tmm-80) REVERT: F 356 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6380 (tp30) REVERT: G 52 ARG cc_start: 0.7424 (mmt180) cc_final: 0.7066 (mmt180) REVERT: G 98 ASP cc_start: 0.8216 (t0) cc_final: 0.7595 (m-30) REVERT: G 302 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6654 (mt-10) REVERT: G 356 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6359 (tp30) REVERT: G 385 ASP cc_start: 0.7797 (p0) cc_final: 0.7574 (p0) REVERT: H 52 ARG cc_start: 0.7485 (mmt180) cc_final: 0.7204 (mmt180) REVERT: H 98 ASP cc_start: 0.8266 (t0) cc_final: 0.7636 (m-30) REVERT: H 173 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7538 (tmm-80) REVERT: H 356 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6343 (tp30) REVERT: H 385 ASP cc_start: 0.7788 (p0) cc_final: 0.7560 (p0) outliers start: 83 outliers final: 45 residues processed: 357 average time/residue: 0.6072 time to fit residues: 245.2785 Evaluate side-chains 356 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 293 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 398 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 206 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 299 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN C 285 GLN D 285 GLN E 176 HIS F 42 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS G 176 HIS H 42 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113700 restraints weight = 25077.606| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.58 r_work: 0.3190 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24648 Z= 0.139 Angle : 0.503 7.789 33392 Z= 0.265 Chirality : 0.045 0.132 3672 Planarity : 0.005 0.046 4448 Dihedral : 5.251 52.631 3545 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.44 % Allowed : 17.43 % Favored : 79.14 % 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: -0.26 (0.14), residues: 3136 helix: 0.63 (0.14), residues: 1312 sheet: 0.94 (0.29), residues: 304 loop : -1.12 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 281 TYR 0.011 0.002 TYR B 333 PHE 0.013 0.001 PHE F 294 TRP 0.007 0.001 TRP H 289 HIS 0.005 0.001 HIS E 271 Details of bonding type rmsd covalent geometry : bond 0.00329 (24608) covalent geometry : angle 0.50269 (33376) SS BOND : bond 0.00312 ( 8) SS BOND : angle 0.73222 ( 16) hydrogen bonds : bond 0.04840 ( 953) hydrogen bonds : angle 3.71518 ( 2670) metal coordination : bond 0.00364 ( 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 377 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 294 time to evaluate : 0.608 Fit side-chains REVERT: A 50 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6361 (mtt90) REVERT: A 116 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7395 (mtpt) REVERT: A 356 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: B 50 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6375 (mtt90) REVERT: B 52 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7619 (mtm110) REVERT: C 50 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6349 (mtt90) REVERT: C 116 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7890 (mtpt) REVERT: C 222 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8036 (ttt180) REVERT: D 50 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6371 (mtt90) REVERT: D 222 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8062 (ttt180) REVERT: E 52 ARG cc_start: 0.7432 (mmt180) cc_final: 0.7162 (mmt180) REVERT: E 98 ASP cc_start: 0.8250 (t0) cc_final: 0.7586 (m-30) REVERT: E 173 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7463 (tmm-80) REVERT: E 302 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6559 (mt-10) REVERT: E 356 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6304 (tp30) REVERT: F 52 ARG cc_start: 0.7480 (mmt180) cc_final: 0.7052 (mmt180) REVERT: F 98 ASP cc_start: 0.8270 (t0) cc_final: 0.7587 (m-30) REVERT: F 173 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7351 (tmm-80) REVERT: F 302 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6562 (mt-10) REVERT: F 356 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6335 (tp30) REVERT: F 385 ASP cc_start: 0.7850 (p0) cc_final: 0.7614 (p0) REVERT: G 52 ARG cc_start: 0.7418 (mmt180) cc_final: 0.7082 (mmt180) REVERT: G 98 ASP cc_start: 0.8260 (t0) cc_final: 0.7585 (m-30) REVERT: G 302 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6633 (mt-10) REVERT: G 356 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6317 (tp30) REVERT: G 385 ASP cc_start: 0.7785 (p0) cc_final: 0.7577 (p0) REVERT: H 52 ARG cc_start: 0.7477 (mmt180) cc_final: 0.7198 (mmt180) REVERT: H 98 ASP cc_start: 0.8267 (t0) cc_final: 0.7597 (m-30) REVERT: H 173 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7478 (tmm-80) REVERT: H 302 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6565 (mt-10) REVERT: H 356 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6311 (tp30) REVERT: H 385 ASP cc_start: 0.7732 (p0) cc_final: 0.7532 (p0) outliers start: 83 outliers final: 51 residues processed: 351 average time/residue: 0.6698 time to fit residues: 265.1496 Evaluate side-chains 357 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 286 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 398 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 39 optimal weight: 10.0000 chunk 209 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 233 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN B 404 ASN C 285 GLN D 285 GLN D 404 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS G 53 GLN G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112895 restraints weight = 25380.333| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.37 r_work: 0.3188 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 24648 Z= 0.228 Angle : 0.591 8.527 33392 Z= 0.317 Chirality : 0.049 0.144 3672 Planarity : 0.006 0.053 4448 Dihedral : 5.665 53.093 3545 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.48 % Allowed : 17.92 % Favored : 78.60 % 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 (0.14), residues: 3136 helix: 0.41 (0.14), residues: 1304 sheet: 1.20 (0.31), residues: 248 loop : -1.30 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 281 TYR 0.013 0.002 TYR B 333 PHE 0.017 0.002 PHE E 294 TRP 0.008 0.002 TRP F 289 HIS 0.007 0.001 HIS E 271 Details of bonding type rmsd covalent geometry : bond 0.00556 (24608) covalent geometry : angle 0.59078 (33376) SS BOND : bond 0.00314 ( 8) SS BOND : angle 0.91768 ( 16) hydrogen bonds : bond 0.06325 ( 953) hydrogen bonds : angle 3.93516 ( 2670) metal coordination : bond 0.00665 ( 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 373 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 289 time to evaluate : 0.716 Fit side-chains REVERT: A 50 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6534 (mtt90) REVERT: A 116 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7664 (mtpt) REVERT: B 50 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6557 (mtt90) REVERT: B 52 ARG cc_start: 0.7884 (mtm110) cc_final: 0.7656 (mtm110) REVERT: C 50 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6530 (mtt90) REVERT: C 116 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8085 (mtpt) REVERT: C 222 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8071 (ttt180) REVERT: D 50 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6519 (mtt90) REVERT: D 222 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8301 (ttt180) REVERT: E 52 ARG cc_start: 0.7448 (mmt180) cc_final: 0.7174 (mmt180) REVERT: E 98 ASP cc_start: 0.8231 (t0) cc_final: 0.7695 (m-30) REVERT: E 173 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7594 (tmm-80) REVERT: E 356 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6377 (tp30) REVERT: F 52 ARG cc_start: 0.7533 (mmt180) cc_final: 0.7120 (mmt180) REVERT: F 98 ASP cc_start: 0.8244 (t0) cc_final: 0.7699 (m-30) REVERT: F 155 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7563 (mptm) REVERT: F 173 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7506 (tmm-80) REVERT: F 356 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6402 (tp30) REVERT: G 52 ARG cc_start: 0.7421 (mmt180) cc_final: 0.7070 (mmt180) REVERT: G 98 ASP cc_start: 0.8249 (t0) cc_final: 0.7694 (m-30) REVERT: G 356 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6376 (tp30) REVERT: H 52 ARG cc_start: 0.7488 (mmt180) cc_final: 0.7208 (mmt180) REVERT: H 98 ASP cc_start: 0.8242 (t0) cc_final: 0.7699 (m-30) REVERT: H 173 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7608 (tmm-80) REVERT: H 356 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6369 (tp30) outliers start: 84 outliers final: 52 residues processed: 346 average time/residue: 0.7198 time to fit residues: 280.1173 Evaluate side-chains 354 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 286 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 398 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 12 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 284 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 305 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 260 optimal weight: 0.7980 chunk 230 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN C 285 GLN C 404 ASN D 285 GLN E 42 HIS E 176 HIS F 176 HIS G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116287 restraints weight = 24888.122| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.58 r_work: 0.3227 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24648 Z= 0.096 Angle : 0.467 7.633 33392 Z= 0.243 Chirality : 0.043 0.129 3672 Planarity : 0.005 0.052 4448 Dihedral : 4.982 54.306 3545 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.57 % Allowed : 18.83 % Favored : 78.60 % 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: -0.11 (0.14), residues: 3136 helix: 0.77 (0.14), residues: 1312 sheet: 1.02 (0.29), residues: 304 loop : -1.05 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 281 TYR 0.009 0.001 TYR B 333 PHE 0.011 0.001 PHE G 294 TRP 0.006 0.001 TRP F 79 HIS 0.006 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00214 (24608) covalent geometry : angle 0.46728 (33376) SS BOND : bond 0.00296 ( 8) SS BOND : angle 0.58570 ( 16) hydrogen bonds : bond 0.03829 ( 953) hydrogen bonds : angle 3.56271 ( 2670) metal coordination : bond 0.00202 ( 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 347 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 285 time to evaluate : 0.902 Fit side-chains REVERT: A 39 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7606 (mtmt) REVERT: A 50 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6313 (mtt90) REVERT: A 116 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7225 (mtpt) REVERT: B 39 LYS cc_start: 0.8126 (mmtm) cc_final: 0.7615 (mtmt) REVERT: B 50 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6359 (mtt90) REVERT: C 39 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7612 (mtmt) REVERT: C 50 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6313 (mtt90) REVERT: C 222 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7956 (ttt180) REVERT: D 39 LYS cc_start: 0.8081 (mmtm) cc_final: 0.7555 (mtmt) REVERT: D 50 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6318 (mtt90) REVERT: D 222 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7983 (ttt180) REVERT: E 52 ARG cc_start: 0.7418 (mmt180) cc_final: 0.7108 (mmt180) REVERT: E 98 ASP cc_start: 0.8239 (t0) cc_final: 0.7571 (m-30) REVERT: E 173 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7384 (tmm-80) REVERT: E 235 LYS cc_start: 0.8330 (mttp) cc_final: 0.8021 (mttm) REVERT: F 52 ARG cc_start: 0.7474 (mmt180) cc_final: 0.7046 (mmt180) REVERT: F 98 ASP cc_start: 0.8238 (t0) cc_final: 0.7564 (m-30) REVERT: F 173 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7377 (tmm-80) REVERT: F 235 LYS cc_start: 0.8316 (mttp) cc_final: 0.8014 (mttm) REVERT: F 385 ASP cc_start: 0.7891 (p0) cc_final: 0.7669 (p0) REVERT: G 98 ASP cc_start: 0.8260 (t0) cc_final: 0.7586 (m-30) REVERT: G 385 ASP cc_start: 0.7870 (p0) cc_final: 0.7218 (t0) REVERT: H 98 ASP cc_start: 0.8254 (t0) cc_final: 0.7583 (m-30) REVERT: H 173 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7450 (tmm-80) REVERT: H 385 ASP cc_start: 0.7893 (p0) cc_final: 0.7662 (p0) outliers start: 62 outliers final: 44 residues processed: 328 average time/residue: 0.6854 time to fit residues: 253.3383 Evaluate side-chains 331 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 277 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 398 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 215 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 257 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 311 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 303 optimal weight: 0.6980 chunk 308 optimal weight: 2.9990 chunk 201 optimal weight: 0.0570 chunk 172 optimal weight: 0.8980 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN C 285 GLN C 404 ASN D 285 GLN E 176 HIS F 176 HIS G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118155 restraints weight = 25042.027| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.37 r_work: 0.3264 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24648 Z= 0.102 Angle : 0.469 8.112 33392 Z= 0.244 Chirality : 0.043 0.127 3672 Planarity : 0.005 0.057 4448 Dihedral : 4.881 52.506 3545 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.40 % Allowed : 19.25 % Favored : 78.35 % 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: 0.91 (0.14), residues: 1320 sheet: 0.72 (0.26), residues: 384 loop : -1.00 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 281 TYR 0.009 0.001 TYR D 333 PHE 0.011 0.001 PHE F 294 TRP 0.006 0.001 TRP F 79 HIS 0.006 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00235 (24608) covalent geometry : angle 0.46899 (33376) SS BOND : bond 0.00263 ( 8) SS BOND : angle 0.53080 ( 16) hydrogen bonds : bond 0.03946 ( 953) hydrogen bonds : angle 3.52564 ( 2670) metal coordination : bond 0.00211 ( 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: 58 poor density : 297 time to evaluate : 0.686 Fit side-chains REVERT: A 39 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7676 (mtmt) REVERT: A 50 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6366 (mtt90) REVERT: A 116 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7246 (mtpt) REVERT: A 281 ARG cc_start: 0.8002 (mtm110) cc_final: 0.7626 (ttp-110) REVERT: A 356 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: B 39 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7673 (mtmt) REVERT: B 50 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6357 (mtt90) REVERT: C 39 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7690 (mtmt) REVERT: C 50 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6368 (mtt90) REVERT: C 222 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7918 (ttt180) REVERT: D 39 LYS cc_start: 0.8142 (mmtm) cc_final: 0.7667 (mtmt) REVERT: D 50 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6343 (mtt90) REVERT: D 155 LYS cc_start: 0.7827 (tptp) cc_final: 0.7416 (tptp) REVERT: D 222 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7986 (ttt180) REVERT: E 52 ARG cc_start: 0.7423 (mmt180) cc_final: 0.7113 (mmt180) REVERT: E 98 ASP cc_start: 0.8174 (t0) cc_final: 0.7565 (m-30) REVERT: E 235 LYS cc_start: 0.8332 (mttp) cc_final: 0.8050 (mttm) REVERT: E 385 ASP cc_start: 0.7893 (p0) cc_final: 0.7672 (p0) REVERT: F 52 ARG cc_start: 0.7477 (mmt180) cc_final: 0.7049 (mmt180) REVERT: F 98 ASP cc_start: 0.8179 (t0) cc_final: 0.7573 (m-30) REVERT: F 173 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7389 (tmm-80) REVERT: F 235 LYS cc_start: 0.8336 (mttp) cc_final: 0.8052 (mttm) REVERT: F 385 ASP cc_start: 0.7954 (p0) cc_final: 0.7275 (t0) REVERT: F 397 ASP cc_start: 0.8371 (m-30) cc_final: 0.8121 (m-30) REVERT: G 52 ARG cc_start: 0.7397 (mmt180) cc_final: 0.7097 (mmt180) REVERT: G 98 ASP cc_start: 0.8199 (t0) cc_final: 0.7568 (m-30) REVERT: G 302 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: G 385 ASP cc_start: 0.7815 (p0) cc_final: 0.7189 (t0) REVERT: G 397 ASP cc_start: 0.8382 (m-30) cc_final: 0.8123 (m-30) REVERT: H 98 ASP cc_start: 0.8193 (t0) cc_final: 0.7573 (m-30) REVERT: H 173 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7478 (tmm-80) REVERT: H 385 ASP cc_start: 0.7784 (p0) cc_final: 0.7216 (t0) outliers start: 58 outliers final: 45 residues processed: 338 average time/residue: 0.7133 time to fit residues: 271.5208 Evaluate side-chains 344 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 288 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 218 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 285 GLN C 285 GLN C 404 ASN D 285 GLN E 176 HIS F 176 HIS G 42 HIS G 176 HIS H 42 HIS H 176 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.115497 restraints weight = 25129.954| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.36 r_work: 0.3226 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24648 Z= 0.153 Angle : 0.527 8.554 33392 Z= 0.276 Chirality : 0.045 0.132 3672 Planarity : 0.005 0.063 4448 Dihedral : 5.206 51.462 3544 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.48 % Allowed : 19.16 % Favored : 78.35 % 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: -0.08 (0.15), residues: 3136 helix: 0.81 (0.14), residues: 1312 sheet: 1.08 (0.29), residues: 304 loop : -1.06 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 281 TYR 0.011 0.002 TYR B 333 PHE 0.013 0.002 PHE E 294 TRP 0.007 0.001 TRP H 289 HIS 0.006 0.001 HIS H 271 Details of bonding type rmsd covalent geometry : bond 0.00367 (24608) covalent geometry : angle 0.52696 (33376) SS BOND : bond 0.00301 ( 8) SS BOND : angle 0.72845 ( 16) hydrogen bonds : bond 0.05035 ( 953) hydrogen bonds : angle 3.70467 ( 2670) metal coordination : bond 0.00406 ( 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 353 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 293 time to evaluate : 0.797 Fit side-chains REVERT: A 50 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6489 (mtt90) REVERT: A 116 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7539 (mtpt) REVERT: A 356 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: B 50 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6540 (mtt90) REVERT: C 50 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6510 (mtt90) REVERT: C 222 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8002 (ttt180) REVERT: D 50 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6530 (mtt90) REVERT: D 222 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8048 (ttt180) REVERT: E 98 ASP cc_start: 0.8246 (t0) cc_final: 0.7663 (m-30) REVERT: E 302 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6649 (mt-10) REVERT: E 385 ASP cc_start: 0.7874 (p0) cc_final: 0.7663 (p0) REVERT: F 52 ARG cc_start: 0.7524 (mmt180) cc_final: 0.7083 (mmt180) REVERT: F 98 ASP cc_start: 0.8262 (t0) cc_final: 0.7676 (m-30) REVERT: F 173 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7528 (tmm-80) REVERT: F 302 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6681 (mt-10) REVERT: F 385 ASP cc_start: 0.7955 (p0) cc_final: 0.7738 (p0) REVERT: G 52 ARG cc_start: 0.7438 (mmt180) cc_final: 0.7126 (mmt180) REVERT: G 98 ASP cc_start: 0.8265 (t0) cc_final: 0.7665 (m-30) REVERT: G 302 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6709 (mt-10) REVERT: G 385 ASP cc_start: 0.7829 (p0) cc_final: 0.7297 (t0) REVERT: H 52 ARG cc_start: 0.7499 (mmt180) cc_final: 0.7237 (mmt180) REVERT: H 98 ASP cc_start: 0.8266 (t0) cc_final: 0.7674 (m-30) REVERT: H 173 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7606 (tmm-80) REVERT: H 302 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6673 (mt-10) REVERT: H 385 ASP cc_start: 0.7802 (p0) cc_final: 0.7277 (t0) outliers start: 60 outliers final: 44 residues processed: 335 average time/residue: 0.7080 time to fit residues: 267.1099 Evaluate side-chains 347 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 289 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 150 optimal weight: 0.0070 chunk 205 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 223 optimal weight: 0.0970 chunk 293 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 285 GLN C 285 GLN D 285 GLN E 176 HIS F 42 HIS F 176 HIS G 176 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115629 restraints weight = 25077.416| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.36 r_work: 0.3228 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24648 Z= 0.147 Angle : 0.521 8.454 33392 Z= 0.273 Chirality : 0.045 0.132 3672 Planarity : 0.005 0.063 4448 Dihedral : 5.201 51.359 3544 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.65 % Allowed : 19.04 % Favored : 78.31 % 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: -0.12 (0.14), residues: 3136 helix: 0.79 (0.14), residues: 1312 sheet: 1.62 (0.31), residues: 248 loop : -1.13 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 281 TYR 0.011 0.002 TYR C 333 PHE 0.014 0.002 PHE H 294 TRP 0.007 0.001 TRP H 289 HIS 0.005 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00351 (24608) covalent geometry : angle 0.52078 (33376) SS BOND : bond 0.00297 ( 8) SS BOND : angle 0.73153 ( 16) hydrogen bonds : bond 0.04904 ( 953) hydrogen bonds : angle 3.69609 ( 2670) metal coordination : bond 0.00397 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7078.29 seconds wall clock time: 121 minutes 4.85 seconds (7264.85 seconds total)