Starting phenix.real_space_refine on Mon Jul 6 14:42:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uhi_42281/07_2026/8uhi_42281_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uhi_42281/07_2026/8uhi_42281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uhi_42281/07_2026/8uhi_42281_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uhi_42281/07_2026/8uhi_42281_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uhi_42281/07_2026/8uhi_42281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uhi_42281/07_2026/8uhi_42281.map" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 104 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 224 5.16 5 C 22936 2.51 5 N 6312 2.21 5 O 7696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37192 Number of models: 1 Model: "" Number of chains: 40 Chain: "I" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "J" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "K" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "L" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "M" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "N" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "O" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "P" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} 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: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} 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: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} 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: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} 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: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} 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: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} 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: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} 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: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} 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: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "K" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "L" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "N" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "O" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "D" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "E" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "F" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "G" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "H" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Time building chain proxies: 8.26, per 1000 atoms: 0.22 Number of scatterers: 37192 At special positions: 0 Unit cell: (127.875, 127.875, 119.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 224 16.00 P 16 15.00 Mg 8 11.99 O 7696 8.00 N 6312 7.00 C 22936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8352 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 40 sheets defined 47.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'I' and resid 20 through 34 Processing helix chain 'I' and resid 65 through 80 removed outlier: 3.838A pdb=" N VAL I 69 " --> pdb=" O ASN I 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 34 Processing helix chain 'J' and resid 65 through 80 removed outlier: 3.834A pdb=" N VAL J 69 " --> pdb=" O ASN J 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 34 Processing helix chain 'K' and resid 65 through 80 removed outlier: 3.840A pdb=" N VAL K 69 " --> pdb=" O ASN K 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 34 Processing helix chain 'L' and resid 65 through 80 removed outlier: 3.836A pdb=" N VAL L 69 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 34 Processing helix chain 'M' and resid 65 through 80 removed outlier: 3.829A pdb=" N VAL M 69 " --> pdb=" O ASN M 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 34 Processing helix chain 'N' and resid 65 through 80 removed outlier: 3.840A pdb=" N VAL N 69 " --> pdb=" O ASN N 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 34 Processing helix chain 'O' and resid 65 through 80 removed outlier: 3.822A pdb=" N VAL O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 34 Processing helix chain 'P' and resid 65 through 80 removed outlier: 3.829A pdb=" N VAL P 69 " --> pdb=" O ASN P 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 26 removed outlier: 3.604A pdb=" N TYR A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 64 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.562A pdb=" N PHE A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 214 through 234 Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'A' and resid 274 through 289 Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.794A pdb=" N ILE A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.651A pdb=" N LEU A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 413 through 435 Processing helix chain 'A' and resid 437 through 453 removed outlier: 6.617A pdb=" N GLY A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 463 Processing helix chain 'B' and resid 21 through 26 removed outlier: 3.604A pdb=" N TYR B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 64 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.562A pdb=" N PHE B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 122 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 155 through 164 Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 214 through 234 Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.794A pdb=" N ILE B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.652A pdb=" N LEU B 315 " --> pdb=" O HIS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 413 through 435 Processing helix chain 'B' and resid 437 through 453 removed outlier: 6.617A pdb=" N GLY B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 463 Processing helix chain 'C' and resid 21 through 26 removed outlier: 3.604A pdb=" N TYR C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 64 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 105 through 109 removed outlier: 3.562A pdb=" N PHE C 109 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 122 Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 155 through 164 Processing helix chain 'C' and resid 182 through 196 Processing helix chain 'C' and resid 214 through 234 Processing helix chain 'C' and resid 247 through 261 Processing helix chain 'C' and resid 274 through 289 Processing helix chain 'C' and resid 298 through 304 removed outlier: 3.794A pdb=" N ILE C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 323 removed outlier: 3.651A pdb=" N LEU C 315 " --> pdb=" O HIS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 352 Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 387 through 395 Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 413 through 435 Processing helix chain 'C' and resid 437 through 453 removed outlier: 6.617A pdb=" N GLY C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP C 444 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 463 Processing helix chain 'D' and resid 21 through 26 removed outlier: 3.604A pdb=" N TYR D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 64 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.562A pdb=" N PHE D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 122 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 214 through 234 Processing helix chain 'D' and resid 247 through 261 Processing helix chain 'D' and resid 274 through 289 Processing helix chain 'D' and resid 298 through 304 removed outlier: 3.794A pdb=" N ILE D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.651A pdb=" N LEU D 315 " --> pdb=" O HIS D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 Processing helix chain 'D' and resid 358 through 362 Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 387 through 395 Processing helix chain 'D' and resid 404 through 409 Processing helix chain 'D' and resid 413 through 435 Processing helix chain 'D' and resid 437 through 453 removed outlier: 6.617A pdb=" N GLY D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 463 Processing helix chain 'E' and resid 21 through 26 removed outlier: 3.604A pdb=" N TYR E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 77 through 81 Processing helix chain 'E' and resid 105 through 109 removed outlier: 3.562A pdb=" N PHE E 109 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 122 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 155 through 164 Processing helix chain 'E' and resid 182 through 196 Processing helix chain 'E' and resid 214 through 234 Processing helix chain 'E' and resid 247 through 261 Processing helix chain 'E' and resid 274 through 289 Processing helix chain 'E' and resid 298 through 304 removed outlier: 3.794A pdb=" N ILE E 302 " --> pdb=" O MET E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 323 removed outlier: 3.652A pdb=" N LEU E 315 " --> pdb=" O HIS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 352 Processing helix chain 'E' and resid 358 through 362 Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 387 through 395 Processing helix chain 'E' and resid 404 through 409 Processing helix chain 'E' and resid 413 through 435 Processing helix chain 'E' and resid 437 through 453 removed outlier: 6.617A pdb=" N GLY E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP E 444 " --> pdb=" O ARG E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 463 Processing helix chain 'F' and resid 21 through 26 removed outlier: 3.604A pdb=" N TYR F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 64 Processing helix chain 'F' and resid 70 through 74 Processing helix chain 'F' and resid 77 through 81 Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.562A pdb=" N PHE F 109 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 Processing helix chain 'F' and resid 124 through 128 Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 155 through 164 Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 214 through 234 Processing helix chain 'F' and resid 247 through 261 Processing helix chain 'F' and resid 274 through 289 Processing helix chain 'F' and resid 298 through 304 removed outlier: 3.794A pdb=" N ILE F 302 " --> pdb=" O MET F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 323 removed outlier: 3.651A pdb=" N LEU F 315 " --> pdb=" O HIS F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 352 Processing helix chain 'F' and resid 358 through 362 Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 387 through 395 Processing helix chain 'F' and resid 404 through 409 Processing helix chain 'F' and resid 413 through 435 Processing helix chain 'F' and resid 437 through 453 removed outlier: 6.617A pdb=" N GLY F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP F 444 " --> pdb=" O ARG F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 463 Processing helix chain 'G' and resid 21 through 26 removed outlier: 3.604A pdb=" N TYR G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 64 Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 77 through 81 Processing helix chain 'G' and resid 105 through 109 removed outlier: 3.562A pdb=" N PHE G 109 " --> pdb=" O LEU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 122 Processing helix chain 'G' and resid 124 through 128 Processing helix chain 'G' and resid 142 through 147 Processing helix chain 'G' and resid 155 through 164 Processing helix chain 'G' and resid 182 through 196 Processing helix chain 'G' and resid 214 through 234 Processing helix chain 'G' and resid 247 through 261 Processing helix chain 'G' and resid 274 through 289 Processing helix chain 'G' and resid 298 through 304 removed outlier: 3.794A pdb=" N ILE G 302 " --> pdb=" O MET G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 323 removed outlier: 3.652A pdb=" N LEU G 315 " --> pdb=" O HIS G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 352 Processing helix chain 'G' and resid 358 through 362 Processing helix chain 'G' and resid 384 through 386 No H-bonds generated for 'chain 'G' and resid 384 through 386' Processing helix chain 'G' and resid 387 through 395 Processing helix chain 'G' and resid 404 through 409 Processing helix chain 'G' and resid 413 through 435 Processing helix chain 'G' and resid 437 through 453 removed outlier: 6.617A pdb=" N GLY G 443 " --> pdb=" O ALA G 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP G 444 " --> pdb=" O ARG G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 463 Processing helix chain 'H' and resid 21 through 26 removed outlier: 3.604A pdb=" N TYR H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 64 Processing helix chain 'H' and resid 70 through 74 Processing helix chain 'H' and resid 77 through 81 Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.562A pdb=" N PHE H 109 " --> pdb=" O LEU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 122 Processing helix chain 'H' and resid 124 through 128 Processing helix chain 'H' and resid 142 through 147 Processing helix chain 'H' and resid 155 through 164 Processing helix chain 'H' and resid 182 through 196 Processing helix chain 'H' and resid 214 through 234 Processing helix chain 'H' and resid 247 through 261 Processing helix chain 'H' and resid 274 through 289 Processing helix chain 'H' and resid 298 through 304 removed outlier: 3.794A pdb=" N ILE H 302 " --> pdb=" O MET H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 323 removed outlier: 3.651A pdb=" N LEU H 315 " --> pdb=" O HIS H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 352 Processing helix chain 'H' and resid 358 through 362 Processing helix chain 'H' and resid 384 through 386 No H-bonds generated for 'chain 'H' and resid 384 through 386' Processing helix chain 'H' and resid 387 through 395 Processing helix chain 'H' and resid 404 through 409 Processing helix chain 'H' and resid 413 through 435 Processing helix chain 'H' and resid 437 through 453 removed outlier: 6.617A pdb=" N GLY H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP H 444 " --> pdb=" O ARG H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 463 Processing sheet with id=AA1, first strand: chain 'I' and resid 54 through 56 removed outlier: 4.870A pdb=" N VAL I 40 " --> pdb=" O TRP I 56 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE I 85 " --> pdb=" O ILE I 102 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE I 102 " --> pdb=" O ILE I 85 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL I 87 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER I 100 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLY I 89 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 54 through 56 removed outlier: 4.854A pdb=" N VAL J 40 " --> pdb=" O TRP J 56 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE J 85 " --> pdb=" O ILE J 102 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE J 102 " --> pdb=" O ILE J 85 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL J 87 " --> pdb=" O SER J 100 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER J 100 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY J 89 " --> pdb=" O ALA J 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 54 through 56 removed outlier: 4.858A pdb=" N VAL K 40 " --> pdb=" O TRP K 56 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE K 85 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE K 102 " --> pdb=" O ILE K 85 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL K 87 " --> pdb=" O SER K 100 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER K 100 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY K 89 " --> pdb=" O ALA K 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 54 through 56 removed outlier: 4.857A pdb=" N VAL L 40 " --> pdb=" O TRP L 56 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE L 85 " --> pdb=" O ILE L 102 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE L 102 " --> pdb=" O ILE L 85 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL L 87 " --> pdb=" O SER L 100 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER L 100 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY L 89 " --> pdb=" O ALA L 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 54 through 56 removed outlier: 4.863A pdb=" N VAL M 40 " --> pdb=" O TRP M 56 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE M 85 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE M 102 " --> pdb=" O ILE M 85 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL M 87 " --> pdb=" O SER M 100 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER M 100 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLY M 89 " --> pdb=" O ALA M 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 54 through 56 removed outlier: 4.857A pdb=" N VAL N 40 " --> pdb=" O TRP N 56 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE N 85 " --> pdb=" O ILE N 102 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE N 102 " --> pdb=" O ILE N 85 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL N 87 " --> pdb=" O SER N 100 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER N 100 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY N 89 " --> pdb=" O ALA N 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 54 through 56 removed outlier: 4.852A pdb=" N VAL O 40 " --> pdb=" O TRP O 56 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE O 85 " --> pdb=" O ILE O 102 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE O 102 " --> pdb=" O ILE O 85 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL O 87 " --> pdb=" O SER O 100 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER O 100 " --> pdb=" O VAL O 87 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY O 89 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 54 through 56 removed outlier: 4.861A pdb=" N VAL P 40 " --> pdb=" O TRP P 56 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE P 85 " --> pdb=" O ILE P 102 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE P 102 " --> pdb=" O ILE P 85 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL P 87 " --> pdb=" O SER P 100 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER P 100 " --> pdb=" O VAL P 87 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY P 89 " --> pdb=" O ALA P 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 90 removed outlier: 6.642A pdb=" N TYR A 101 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE A 88 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 99 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 138 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A 42 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU A 136 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR A 44 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU A 134 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N GLY A 309 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 134 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.459A pdb=" N LEU A 170 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA A 377 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN A 402 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA A 379 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 327 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER A 380 " --> pdb=" O ILE A 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 200 through 202 removed outlier: 6.948A pdb=" N THR A 201 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN A 242 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS A 239 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET A 267 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU A 241 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP A 269 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 266 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N HIS A 295 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS A 268 " --> pdb=" O HIS A 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AB4, first strand: chain 'B' and resid 84 through 90 removed outlier: 6.642A pdb=" N TYR B 101 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE B 88 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 99 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 138 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG B 42 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU B 136 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR B 44 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU B 134 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N GLY B 309 " --> pdb=" O ARG B 132 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 134 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.459A pdb=" N LEU B 170 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA B 377 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN B 402 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA B 379 " --> pdb=" O GLN B 402 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 327 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER B 380 " --> pdb=" O ILE B 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 200 through 202 removed outlier: 6.948A pdb=" N THR B 201 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN B 242 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS B 239 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET B 267 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU B 241 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP B 269 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL B 266 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N HIS B 295 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS B 268 " --> pdb=" O HIS B 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AB8, first strand: chain 'C' and resid 84 through 90 removed outlier: 6.642A pdb=" N TYR C 101 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE C 88 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 99 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 138 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG C 42 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU C 136 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR C 44 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU C 134 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N GLY C 309 " --> pdb=" O ARG C 132 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU C 134 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 170 through 172 removed outlier: 6.459A pdb=" N LEU C 170 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA C 377 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN C 402 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA C 379 " --> pdb=" O GLN C 402 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE C 327 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER C 380 " --> pdb=" O ILE C 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 200 through 202 removed outlier: 6.948A pdb=" N THR C 201 " --> pdb=" O TYR C 240 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN C 242 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS C 239 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET C 267 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU C 241 " --> pdb=" O MET C 267 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP C 269 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL C 266 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N HIS C 295 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS C 268 " --> pdb=" O HIS C 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC3, first strand: chain 'D' and resid 84 through 90 removed outlier: 6.642A pdb=" N TYR D 101 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE D 88 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE D 99 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP D 138 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG D 42 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU D 136 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR D 44 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU D 134 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N GLY D 309 " --> pdb=" O ARG D 132 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU D 134 " --> pdb=" O GLY D 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.458A pdb=" N LEU D 170 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA D 377 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN D 402 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA D 379 " --> pdb=" O GLN D 402 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE D 327 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER D 380 " --> pdb=" O ILE D 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 200 through 202 removed outlier: 6.948A pdb=" N THR D 201 " --> pdb=" O TYR D 240 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN D 242 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS D 239 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET D 267 " --> pdb=" O HIS D 239 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU D 241 " --> pdb=" O MET D 267 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP D 269 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL D 266 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N HIS D 295 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS D 268 " --> pdb=" O HIS D 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 354 through 355 Processing sheet with id=AC7, first strand: chain 'E' and resid 84 through 90 removed outlier: 6.642A pdb=" N TYR E 101 " --> pdb=" O TYR E 86 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE E 88 " --> pdb=" O ILE E 99 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE E 99 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP E 138 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG E 42 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU E 136 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR E 44 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU E 134 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N GLY E 309 " --> pdb=" O ARG E 132 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU E 134 " --> pdb=" O GLY E 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 170 through 172 removed outlier: 6.459A pdb=" N LEU E 170 " --> pdb=" O LEU E 401 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA E 377 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN E 402 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA E 379 " --> pdb=" O GLN E 402 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE E 327 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N SER E 380 " --> pdb=" O ILE E 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 200 through 202 removed outlier: 6.948A pdb=" N THR E 201 " --> pdb=" O TYR E 240 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN E 242 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS E 239 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET E 267 " --> pdb=" O HIS E 239 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU E 241 " --> pdb=" O MET E 267 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP E 269 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL E 266 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N HIS E 295 " --> pdb=" O VAL E 266 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS E 268 " --> pdb=" O HIS E 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 354 through 355 Processing sheet with id=AD2, first strand: chain 'F' and resid 84 through 90 removed outlier: 6.642A pdb=" N TYR F 101 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE F 88 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE F 99 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP F 138 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG F 42 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU F 136 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR F 44 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU F 134 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N GLY F 309 " --> pdb=" O ARG F 132 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU F 134 " --> pdb=" O GLY F 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 170 through 172 removed outlier: 6.459A pdb=" N LEU F 170 " --> pdb=" O LEU F 401 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA F 377 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN F 402 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA F 379 " --> pdb=" O GLN F 402 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE F 327 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER F 380 " --> pdb=" O ILE F 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 200 through 202 removed outlier: 6.948A pdb=" N THR F 201 " --> pdb=" O TYR F 240 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN F 242 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS F 239 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET F 267 " --> pdb=" O HIS F 239 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU F 241 " --> pdb=" O MET F 267 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP F 269 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL F 266 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N HIS F 295 " --> pdb=" O VAL F 266 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS F 268 " --> pdb=" O HIS F 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'F' and resid 354 through 355 Processing sheet with id=AD6, first strand: chain 'G' and resid 84 through 90 removed outlier: 6.642A pdb=" N TYR G 101 " --> pdb=" O TYR G 86 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE G 88 " --> pdb=" O ILE G 99 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE G 99 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP G 138 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG G 42 " --> pdb=" O LEU G 136 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU G 136 " --> pdb=" O ARG G 42 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR G 44 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU G 134 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N GLY G 309 " --> pdb=" O ARG G 132 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU G 134 " --> pdb=" O GLY G 309 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 170 through 172 removed outlier: 6.459A pdb=" N LEU G 170 " --> pdb=" O LEU G 401 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA G 377 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN G 402 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA G 379 " --> pdb=" O GLN G 402 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE G 327 " --> pdb=" O VAL G 378 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER G 380 " --> pdb=" O ILE G 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 200 through 202 removed outlier: 6.948A pdb=" N THR G 201 " --> pdb=" O TYR G 240 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN G 242 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS G 239 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET G 267 " --> pdb=" O HIS G 239 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU G 241 " --> pdb=" O MET G 267 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP G 269 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL G 266 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N HIS G 295 " --> pdb=" O VAL G 266 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N HIS G 268 " --> pdb=" O HIS G 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'G' and resid 354 through 355 Processing sheet with id=AE1, first strand: chain 'H' and resid 84 through 90 removed outlier: 6.642A pdb=" N TYR H 101 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE H 88 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE H 99 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP H 138 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG H 42 " --> pdb=" O LEU H 136 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU H 136 " --> pdb=" O ARG H 42 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR H 44 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU H 134 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N GLY H 309 " --> pdb=" O ARG H 132 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU H 134 " --> pdb=" O GLY H 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 170 through 172 removed outlier: 6.459A pdb=" N LEU H 170 " --> pdb=" O LEU H 401 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA H 377 " --> pdb=" O VAL H 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN H 402 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA H 379 " --> pdb=" O GLN H 402 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE H 327 " --> pdb=" O VAL H 378 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER H 380 " --> pdb=" O ILE H 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'H' and resid 200 through 202 removed outlier: 6.948A pdb=" N THR H 201 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN H 242 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS H 239 " --> pdb=" O ILE H 265 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET H 267 " --> pdb=" O HIS H 239 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU H 241 " --> pdb=" O MET H 267 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP H 269 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL H 266 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N HIS H 295 " --> pdb=" O VAL H 266 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS H 268 " --> pdb=" O HIS H 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'H' and resid 354 through 355 1616 hydrogen bonds defined for protein. 4440 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: 10.44 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6088 1.31 - 1.44: 10264 1.44 - 1.57: 20464 1.57 - 1.69: 16 1.69 - 1.82: 336 Bond restraints: 37168 Sorted by residual: bond pdb=" O5P RUB H 501 " pdb=" P2 RUB H 501 " ideal model delta sigma weight residual 1.671 1.506 0.165 2.00e-02 2.50e+03 6.84e+01 bond pdb=" O5P RUB B 501 " pdb=" P2 RUB B 501 " ideal model delta sigma weight residual 1.671 1.506 0.165 2.00e-02 2.50e+03 6.84e+01 bond pdb=" O5P RUB F 501 " pdb=" P2 RUB F 501 " ideal model delta sigma weight residual 1.671 1.506 0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" O5P RUB D 501 " pdb=" P2 RUB D 501 " ideal model delta sigma weight residual 1.671 1.506 0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" O5P RUB E 501 " pdb=" P2 RUB E 501 " ideal model delta sigma weight residual 1.671 1.509 0.162 2.00e-02 2.50e+03 6.59e+01 ... (remaining 37163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.99: 50400 10.99 - 21.98: 40 21.98 - 32.97: 0 32.97 - 43.96: 0 43.96 - 54.95: 16 Bond angle restraints: 50456 Sorted by residual: angle pdb=" O4P RUB C 501 " pdb=" P2 RUB C 501 " pdb=" O5P RUB C 501 " ideal model delta sigma weight residual 54.51 109.46 -54.95 3.00e+00 1.11e-01 3.36e+02 angle pdb=" O4P RUB E 501 " pdb=" P2 RUB E 501 " pdb=" O5P RUB E 501 " ideal model delta sigma weight residual 54.51 109.46 -54.95 3.00e+00 1.11e-01 3.36e+02 angle pdb=" O4P RUB A 501 " pdb=" P2 RUB A 501 " pdb=" O5P RUB A 501 " ideal model delta sigma weight residual 54.51 109.46 -54.95 3.00e+00 1.11e-01 3.36e+02 angle pdb=" O4P RUB G 501 " pdb=" P2 RUB G 501 " pdb=" O5P RUB G 501 " ideal model delta sigma weight residual 54.51 109.46 -54.95 3.00e+00 1.11e-01 3.36e+02 angle pdb=" O4P RUB D 501 " pdb=" P2 RUB D 501 " pdb=" O5P RUB D 501 " ideal model delta sigma weight residual 54.51 109.46 -54.95 3.00e+00 1.11e-01 3.36e+02 ... (remaining 50451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 18708 17.20 - 34.40: 2345 34.40 - 51.60: 679 51.60 - 68.80: 221 68.80 - 86.00: 63 Dihedral angle restraints: 22016 sinusoidal: 8904 harmonic: 13112 Sorted by residual: dihedral pdb=" CA TYR M 52 " pdb=" C TYR M 52 " pdb=" N TRP M 53 " pdb=" CA TRP M 53 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA TYR I 52 " pdb=" C TYR I 52 " pdb=" N TRP I 53 " pdb=" CA TRP I 53 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TYR P 52 " pdb=" C TYR P 52 " pdb=" N TRP P 53 " pdb=" CA TRP P 53 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 22013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3795 0.044 - 0.089: 1260 0.089 - 0.133: 273 0.133 - 0.177: 32 0.177 - 0.221: 16 Chirality restraints: 5376 Sorted by residual: chirality pdb=" C4 RUB C 501 " pdb=" C3 RUB C 501 " pdb=" C5 RUB C 501 " pdb=" O4 RUB C 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.46 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C4 RUB F 501 " pdb=" C3 RUB F 501 " pdb=" C5 RUB F 501 " pdb=" O4 RUB F 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.46 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C4 RUB H 501 " pdb=" C3 RUB H 501 " pdb=" C5 RUB H 501 " pdb=" O4 RUB H 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.47 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 5373 not shown) Planarity restraints: 6600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 89 " 0.037 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO G 90 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 90 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 90 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 89 " -0.037 5.00e-02 4.00e+02 5.28e-02 4.45e+00 pdb=" N PRO D 90 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 90 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 90 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 89 " -0.036 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO F 90 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO F 90 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 90 " -0.029 5.00e-02 4.00e+02 ... (remaining 6597 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 1 1.94 - 2.68: 1550 2.68 - 3.42: 57275 3.42 - 4.16: 113959 4.16 - 4.90: 187977 Nonbonded interactions: 360762 Sorted by model distance: nonbonded pdb=" O HOH H 625 " pdb=" O HOH H 671 " model vdw 1.205 3.040 nonbonded pdb=" O3 RUB G 501 " pdb="MG MG G 502 " model vdw 1.989 2.170 nonbonded pdb=" O3 RUB D 501 " pdb="MG MG D 502 " model vdw 1.989 2.170 nonbonded pdb=" O3 RUB B 501 " pdb="MG MG B 502 " model vdw 1.989 2.170 nonbonded pdb=" O3 RUB A 501 " pdb="MG MG A 502 " model vdw 1.989 2.170 ... (remaining 360757 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: 0.01 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' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 36.550 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.220 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:10.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 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 : 0.007 0.165 37168 Z= 0.329 Angle : 1.327 54.952 50456 Z= 0.534 Chirality : 0.046 0.221 5376 Planarity : 0.006 0.053 6600 Dihedral : 17.604 86.002 13664 Min Nonbonded Distance : 1.205 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.84 % Allowed : 22.01 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: -0.14 (0.12), residues: 4520 helix: 0.78 (0.12), residues: 1776 sheet: -0.63 (0.19), residues: 696 loop : -0.57 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 132 TYR 0.021 0.002 TYR I 36 PHE 0.027 0.002 PHE G 346 TRP 0.014 0.002 TRP F 67 HIS 0.016 0.002 HIS M 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.33 (37168) covalent geometry : angle 1.32745 / 0.53 (50456) hydrogen bonds : bond 0.12978 / 8.57 ( 1616) hydrogen bonds : angle 6.20805 / 4.28 ( 4440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 620 time to evaluate : 1.123 Fit side-chains REVERT: A 260 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: D 260 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: E 260 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: F 260 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: G 260 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: H 260 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6927 (tt0) outliers start: 69 outliers final: 55 residues processed: 667 average time/residue: 0.7990 time to fit residues: 633.6624 Evaluate side-chains 680 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 619 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 173 CYS Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 173 CYS Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 475 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 8.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 43 ASN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 ASN ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** K 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 HIS L 43 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 HIS M 43 ASN ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 HIS N 43 ASN N 95 GLN N 104 HIS O 43 ASN ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 HIS P 43 ASN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN A 154 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN A 278 ASN A 283 HIS A 387 HIS A 433 ASN B 150 GLN B 154 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN B 278 ASN B 283 HIS B 387 HIS B 433 ASN C 150 GLN C 154 HIS C 206 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN C 278 ASN C 283 HIS C 387 HIS C 433 ASN D 150 GLN D 154 HIS ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN D 278 ASN D 283 HIS D 387 HIS D 433 ASN E 150 GLN E 154 HIS ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN E 278 ASN E 283 HIS E 387 HIS E 433 ASN F 150 GLN F 154 HIS ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN F 278 ASN F 283 HIS F 387 HIS F 433 ASN G 150 GLN G 154 HIS ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 ASN G 278 ASN G 283 HIS G 387 HIS G 433 ASN H 150 GLN H 154 HIS ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 ASN H 278 ASN H 283 HIS H 387 HIS H 433 ASN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.185172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.168520 restraints weight = 30488.869| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 0.53 r_work: 0.3625 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 37168 Z= 0.228 Angle : 0.675 6.905 50456 Z= 0.359 Chirality : 0.046 0.170 5376 Planarity : 0.005 0.039 6600 Dihedral : 9.145 74.465 5361 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.05 % Allowed : 18.82 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: -0.21 (0.12), residues: 4520 helix: 0.76 (0.12), residues: 1792 sheet: -0.92 (0.17), residues: 792 loop : -0.53 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 254 TYR 0.018 0.002 TYR I 10 PHE 0.025 0.003 PHE E 346 TRP 0.010 0.002 TRP G 67 HIS 0.010 0.002 HIS F 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (37168) covalent geometry : angle 0.67503 / 0.36 (50456) hydrogen bonds : bond 0.04793 / 3.10 ( 1616) hydrogen bonds : angle 5.21078 / 3.59 ( 4440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 639 time to evaluate : 1.476 Fit side-chains REVERT: I 6 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7314 (mttt) REVERT: I 70 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6619 (tp) REVERT: I 72 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.5811 (mm-30) REVERT: J 70 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6694 (tp) REVERT: J 72 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.5920 (mt-10) REVERT: K 70 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6704 (tp) REVERT: K 72 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5799 (mm-30) REVERT: L 70 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6641 (tp) REVERT: L 72 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.5731 (mm-30) REVERT: M 25 GLU cc_start: 0.6040 (OUTLIER) cc_final: 0.5742 (mm-30) REVERT: M 70 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6655 (tp) REVERT: M 72 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5808 (mm-30) REVERT: N 70 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6698 (tp) REVERT: N 72 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5804 (mm-30) REVERT: O 25 GLU cc_start: 0.5905 (OUTLIER) cc_final: 0.5661 (mm-30) REVERT: O 70 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6661 (tp) REVERT: O 72 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.6044 (mt-10) REVERT: P 25 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.5687 (mm-30) REVERT: P 70 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6659 (tp) REVERT: P 72 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5789 (mm-30) REVERT: A 448 GLU cc_start: 0.5921 (pt0) cc_final: 0.5716 (pt0) REVERT: A 467 LYS cc_start: 0.5478 (tttp) cc_final: 0.4621 (tptt) REVERT: B 448 GLU cc_start: 0.5896 (pt0) cc_final: 0.5686 (pt0) REVERT: B 467 LYS cc_start: 0.5498 (tttp) cc_final: 0.4656 (tptt) REVERT: C 467 LYS cc_start: 0.5497 (tttp) cc_final: 0.4646 (tptt) REVERT: D 448 GLU cc_start: 0.5913 (pt0) cc_final: 0.5712 (pt0) REVERT: D 467 LYS cc_start: 0.5507 (tttp) cc_final: 0.4672 (tptt) REVERT: E 467 LYS cc_start: 0.5447 (tttp) cc_final: 0.4582 (tptt) REVERT: F 448 GLU cc_start: 0.5923 (pt0) cc_final: 0.5721 (pt0) REVERT: F 467 LYS cc_start: 0.5500 (tttp) cc_final: 0.4653 (tptt) REVERT: G 448 GLU cc_start: 0.5907 (pt0) cc_final: 0.5701 (pt0) REVERT: G 467 LYS cc_start: 0.5510 (tttp) cc_final: 0.4672 (tptt) REVERT: H 467 LYS cc_start: 0.5522 (tttp) cc_final: 0.4679 (tptt) outliers start: 152 outliers final: 56 residues processed: 708 average time/residue: 0.8117 time to fit residues: 681.0645 Evaluate side-chains 683 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 607 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 72 GLU Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 86 ARG Chi-restraints excluded: chain P residue 25 GLU Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 173 CYS Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 173 CYS Chi-restraints excluded: chain H residue 475 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 172 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 403 optimal weight: 9.9990 chunk 429 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 399 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 chunk 360 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 95 GLN J 95 GLN K 95 GLN L 95 GLN L 104 HIS M 95 GLN M 104 HIS O 95 GLN O 104 HIS P 95 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.185352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.168619 restraints weight = 30427.238| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 0.55 r_work: 0.3625 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 37168 Z= 0.217 Angle : 0.649 6.686 50456 Z= 0.346 Chirality : 0.046 0.168 5376 Planarity : 0.005 0.036 6600 Dihedral : 8.522 60.446 5327 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.61 % Allowed : 18.36 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: -0.24 (0.12), residues: 4520 helix: 0.72 (0.12), residues: 1792 sheet: -0.86 (0.17), residues: 792 loop : -0.56 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 132 TYR 0.018 0.002 TYR I 10 PHE 0.025 0.003 PHE E 346 TRP 0.010 0.002 TRP D 369 HIS 0.008 0.002 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (37168) covalent geometry : angle 0.64859 / 0.35 (50456) hydrogen bonds : bond 0.04640 / 2.99 ( 1616) hydrogen bonds : angle 5.07837 / 3.50 ( 4440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 663 time to evaluate : 1.456 Fit side-chains REVERT: I 70 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6661 (tp) REVERT: I 72 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5816 (mm-30) REVERT: J 25 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5713 (mm-30) REVERT: J 26 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6622 (mtpt) REVERT: J 70 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6649 (tp) REVERT: J 72 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.5737 (mm-30) REVERT: K 25 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.5710 (mm-30) REVERT: K 26 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6636 (mtpt) REVERT: K 70 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6683 (tp) REVERT: K 72 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5752 (mm-30) REVERT: K 77 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6430 (ttm170) REVERT: L 26 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6600 (mtpt) REVERT: L 70 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6643 (tp) REVERT: L 72 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5699 (mm-30) REVERT: M 25 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5719 (mm-30) REVERT: M 70 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6675 (tp) REVERT: M 72 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5747 (mm-30) REVERT: N 25 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5718 (mm-30) REVERT: N 26 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6628 (mtpt) REVERT: N 70 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6676 (tp) REVERT: N 72 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5829 (mm-30) REVERT: O 70 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6685 (tp) REVERT: O 72 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.6031 (mt-10) REVERT: P 25 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5709 (mm-30) REVERT: P 70 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6677 (tp) REVERT: P 72 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5805 (mm-30) REVERT: A 179 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6728 (mp) REVERT: B 179 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6735 (mp) REVERT: C 179 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6736 (mp) REVERT: D 179 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6735 (mp) REVERT: E 179 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6704 (mp) REVERT: F 179 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6739 (mp) REVERT: G 179 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6725 (mp) REVERT: H 179 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6732 (mp) outliers start: 173 outliers final: 56 residues processed: 728 average time/residue: 0.7715 time to fit residues: 667.0627 Evaluate side-chains 703 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 613 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain J residue 25 GLU Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 77 ARG Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 26 LYS Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 72 GLU Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain P residue 25 GLU Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 340 ARG Chi-restraints excluded: chain H residue 475 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 280 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 394 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 435 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 275 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 104 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 HIS ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.183162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.166121 restraints weight = 30340.751| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 0.59 r_work: 0.3619 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 37168 Z= 0.309 Angle : 0.746 6.311 50456 Z= 0.401 Chirality : 0.050 0.178 5376 Planarity : 0.006 0.036 6600 Dihedral : 8.581 63.814 5312 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.69 % Allowed : 18.76 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: -0.55 (0.12), residues: 4520 helix: 0.28 (0.11), residues: 1792 sheet: -0.80 (0.18), residues: 712 loop : -0.66 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 132 TYR 0.020 0.003 TYR L 10 PHE 0.023 0.004 PHE A 346 TRP 0.012 0.003 TRP E 369 HIS 0.010 0.002 HIS D 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.31 (37168) covalent geometry : angle 0.74616 / 0.40 (50456) hydrogen bonds : bond 0.05307 / 3.43 ( 1616) hydrogen bonds : angle 5.33142 / 3.68 ( 4440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 657 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 70 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6657 (tp) REVERT: J 25 GLU cc_start: 0.5903 (OUTLIER) cc_final: 0.5664 (mm-30) REVERT: J 70 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6676 (tp) REVERT: K 25 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.5664 (mm-30) REVERT: K 70 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6660 (tp) REVERT: L 25 GLU cc_start: 0.5896 (OUTLIER) cc_final: 0.5649 (mm-30) REVERT: L 70 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6671 (tp) REVERT: M 25 GLU cc_start: 0.5998 (OUTLIER) cc_final: 0.5701 (mm-30) REVERT: M 70 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6684 (tp) REVERT: N 25 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.5660 (mm-30) REVERT: N 70 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6693 (tp) REVERT: O 70 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6708 (tp) REVERT: O 72 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.6103 (mt-10) REVERT: P 25 GLU cc_start: 0.5894 (OUTLIER) cc_final: 0.5650 (mm-30) REVERT: P 70 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6678 (tp) REVERT: A 179 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6832 (mp) REVERT: B 179 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.6841 (mp) REVERT: C 179 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6835 (mp) REVERT: D 179 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6834 (mp) REVERT: E 179 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6818 (mp) REVERT: F 139 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8572 (mp) REVERT: F 179 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6836 (mp) REVERT: G 179 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6827 (mp) REVERT: H 179 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.6832 (mp) outliers start: 176 outliers final: 82 residues processed: 721 average time/residue: 0.8363 time to fit residues: 717.5986 Evaluate side-chains 733 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 627 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain J residue 25 GLU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 25 GLU Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 72 GLU Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain P residue 25 GLU Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 80 ARG Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 34 ASP Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 359 LYS Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 34 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain H residue 475 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 203 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 351 optimal weight: 5.9990 chunk 423 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 400 optimal weight: 1.9990 chunk 299 optimal weight: 0.8980 chunk 367 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 318 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 104 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 HIS ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 305 GLN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 305 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.186162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.168862 restraints weight = 30407.313| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 0.62 r_work: 0.3614 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 37168 Z= 0.180 Angle : 0.612 6.693 50456 Z= 0.326 Chirality : 0.044 0.164 5376 Planarity : 0.005 0.033 6600 Dihedral : 8.253 61.416 5312 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.52 % Allowed : 20.60 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: -0.17 (0.12), residues: 4520 helix: 0.75 (0.12), residues: 1792 sheet: -0.63 (0.19), residues: 712 loop : -0.60 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 132 TYR 0.020 0.002 TYR I 10 PHE 0.026 0.002 PHE B 346 TRP 0.011 0.002 TRP F 369 HIS 0.009 0.002 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (37168) covalent geometry : angle 0.61211 / 0.33 (50456) hydrogen bonds : bond 0.04314 / 2.78 ( 1616) hydrogen bonds : angle 4.93812 / 3.40 ( 4440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 661 time to evaluate : 1.508 Fit side-chains REVERT: I 70 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6578 (tp) REVERT: I 72 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.5846 (mm-30) REVERT: J 70 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6619 (tp) REVERT: J 72 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5756 (mm-30) REVERT: K 70 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6660 (tp) REVERT: K 72 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.5865 (mm-30) REVERT: L 70 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6618 (tp) REVERT: L 72 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.5856 (mm-30) REVERT: L 77 ARG cc_start: 0.6878 (ttm110) cc_final: 0.6661 (ttm170) REVERT: M 25 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5761 (mm-30) REVERT: M 70 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6612 (tp) REVERT: M 72 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.5850 (mm-30) REVERT: N 70 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6634 (tp) REVERT: N 72 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5888 (mm-30) REVERT: O 25 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5570 (tp30) REVERT: O 70 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6613 (tp) REVERT: O 72 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.6042 (mt-10) REVERT: P 25 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5737 (mm-30) REVERT: P 70 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6610 (tp) REVERT: P 72 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.5879 (mm-30) REVERT: B 260 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: C 260 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7747 (tt0) outliers start: 132 outliers final: 54 residues processed: 716 average time/residue: 0.8137 time to fit residues: 692.6483 Evaluate side-chains 712 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 637 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 72 GLU Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain P residue 25 GLU Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 475 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 265 optimal weight: 10.0000 chunk 374 optimal weight: 0.7980 chunk 216 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 319 optimal weight: 4.9990 chunk 369 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 chunk 239 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 104 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 HIS ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS ** H 239 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 = 0.3966 r_free = 0.3966 target = 0.184524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.167200 restraints weight = 30302.024| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 0.62 r_work: 0.3598 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 37168 Z= 0.239 Angle : 0.673 6.356 50456 Z= 0.360 Chirality : 0.046 0.171 5376 Planarity : 0.005 0.032 6600 Dihedral : 8.382 63.000 5312 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.40 % Allowed : 19.54 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: -0.34 (0.12), residues: 4520 helix: 0.57 (0.12), residues: 1792 sheet: -0.69 (0.19), residues: 712 loop : -0.66 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 132 TYR 0.018 0.002 TYR I 10 PHE 0.025 0.003 PHE B 346 TRP 0.011 0.002 TRP B 452 HIS 0.011 0.002 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 (37168) covalent geometry : angle 0.67310 / 0.36 (50456) hydrogen bonds : bond 0.04803 / 3.10 ( 1616) hydrogen bonds : angle 5.11011 / 3.52 ( 4440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 639 time to evaluate : 1.480 Fit side-chains REVERT: I 70 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6620 (tp) REVERT: I 72 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5825 (mm-30) REVERT: J 25 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5709 (mm-30) REVERT: J 70 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6621 (tp) REVERT: J 72 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5818 (mm-30) REVERT: K 25 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5717 (mm-30) REVERT: K 70 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6659 (tp) REVERT: K 72 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5833 (mm-30) REVERT: L 25 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5696 (mm-30) REVERT: L 70 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6633 (tp) REVERT: L 72 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5811 (mm-30) REVERT: M 25 GLU cc_start: 0.6034 (OUTLIER) cc_final: 0.5734 (mm-30) REVERT: M 70 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6630 (tp) REVERT: M 72 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.5815 (mm-30) REVERT: N 25 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5705 (mm-30) REVERT: N 70 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6638 (tp) REVERT: N 72 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5832 (mm-30) REVERT: O 70 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6655 (tp) REVERT: O 72 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6153 (mt-10) REVERT: P 25 GLU cc_start: 0.5966 (OUTLIER) cc_final: 0.5715 (mm-30) REVERT: P 70 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6625 (tp) REVERT: P 72 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5841 (mm-30) REVERT: A 179 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6780 (mp) REVERT: B 179 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6788 (mp) REVERT: C 179 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6785 (mp) REVERT: D 179 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6781 (mp) REVERT: D 452 TRP cc_start: 0.4416 (t60) cc_final: 0.4206 (t60) REVERT: E 179 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6765 (mp) REVERT: F 179 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6785 (mp) REVERT: F 452 TRP cc_start: 0.4440 (t60) cc_final: 0.4230 (t60) REVERT: G 179 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6773 (mp) REVERT: G 452 TRP cc_start: 0.4402 (t60) cc_final: 0.4192 (t60) REVERT: H 179 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6794 (mp) outliers start: 165 outliers final: 88 residues processed: 706 average time/residue: 0.8387 time to fit residues: 702.2762 Evaluate side-chains 747 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 629 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain J residue 25 GLU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 25 GLU Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 72 GLU Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain P residue 25 GLU Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 80 ARG Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 359 LYS Chi-restraints excluded: chain F residue 371 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain H residue 475 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 268 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 430 optimal weight: 7.9990 chunk 271 optimal weight: 6.9990 chunk 354 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 310 optimal weight: 9.9990 chunk 287 optimal weight: 5.9990 chunk 414 optimal weight: 10.0000 chunk 294 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 104 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 HIS ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS ** H 239 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 = 0.3971 r_free = 0.3971 target = 0.185005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.167318 restraints weight = 30398.389| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 0.64 r_work: 0.3599 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 37168 Z= 0.224 Angle : 0.658 6.429 50456 Z= 0.352 Chirality : 0.046 0.169 5376 Planarity : 0.005 0.034 6600 Dihedral : 8.320 62.354 5312 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.26 % Allowed : 19.70 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: -0.33 (0.12), residues: 4520 helix: 0.58 (0.12), residues: 1792 sheet: -0.68 (0.19), residues: 712 loop : -0.67 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 132 TYR 0.024 0.002 TYR K 36 PHE 0.025 0.003 PHE B 346 TRP 0.011 0.002 TRP A 369 HIS 0.011 0.002 HIS D 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (37168) covalent geometry : angle 0.65803 / 0.35 (50456) hydrogen bonds : bond 0.04663 / 3.01 ( 1616) hydrogen bonds : angle 5.03347 / 3.47 ( 4440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 640 time to evaluate : 1.491 Fit side-chains REVERT: I 70 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6602 (tp) REVERT: I 72 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5887 (mm-30) REVERT: J 25 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5714 (mm-30) REVERT: J 70 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6613 (tp) REVERT: J 72 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.5804 (mm-30) REVERT: K 25 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.5735 (mm-30) REVERT: K 70 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6640 (tp) REVERT: K 72 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.5887 (mm-30) REVERT: L 25 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5687 (mm-30) REVERT: L 70 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6615 (tp) REVERT: L 72 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5824 (mm-30) REVERT: M 25 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5717 (mm-30) REVERT: M 70 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6619 (tp) REVERT: M 72 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5840 (mm-30) REVERT: N 25 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5719 (mm-30) REVERT: N 70 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6625 (tp) REVERT: N 72 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.5916 (mm-30) REVERT: O 70 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6650 (tp) REVERT: O 72 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.6116 (mt-10) REVERT: P 70 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6631 (tp) REVERT: P 72 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.5909 (mm-30) REVERT: A 179 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6769 (mp) REVERT: A 337 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5877 (tt0) REVERT: A 467 LYS cc_start: 0.5627 (tttp) cc_final: 0.4713 (tptt) REVERT: B 179 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6774 (mp) REVERT: B 337 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5887 (tt0) REVERT: B 467 LYS cc_start: 0.5589 (tttp) cc_final: 0.4670 (tptt) REVERT: C 179 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.6777 (mp) REVERT: C 337 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5878 (tt0) REVERT: C 467 LYS cc_start: 0.5596 (tttp) cc_final: 0.4685 (tptt) REVERT: D 179 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6764 (mp) REVERT: D 337 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5895 (tt0) REVERT: D 452 TRP cc_start: 0.4486 (t60) cc_final: 0.4234 (t60) REVERT: D 467 LYS cc_start: 0.5626 (tttp) cc_final: 0.4723 (tptt) REVERT: E 179 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6752 (mp) REVERT: E 337 GLU cc_start: 0.6186 (OUTLIER) cc_final: 0.5882 (tt0) REVERT: E 467 LYS cc_start: 0.5587 (tttp) cc_final: 0.4669 (tptt) REVERT: F 179 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6775 (mp) REVERT: F 337 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5867 (tt0) REVERT: F 452 TRP cc_start: 0.4507 (t60) cc_final: 0.4251 (t60) REVERT: F 467 LYS cc_start: 0.5594 (tttp) cc_final: 0.4685 (tptt) REVERT: G 179 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6763 (mp) REVERT: G 337 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5897 (tt0) REVERT: G 452 TRP cc_start: 0.4481 (t60) cc_final: 0.4228 (t60) REVERT: G 467 LYS cc_start: 0.5639 (tttp) cc_final: 0.4743 (tptt) REVERT: H 179 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6780 (mp) REVERT: H 337 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.5876 (tt0) REVERT: H 467 LYS cc_start: 0.5601 (tttp) cc_final: 0.4683 (tptt) outliers start: 160 outliers final: 95 residues processed: 712 average time/residue: 0.8502 time to fit residues: 716.7146 Evaluate side-chains 755 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 623 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain J residue 25 GLU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 25 GLU Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 72 GLU Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 80 ARG Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 359 LYS Chi-restraints excluded: chain F residue 371 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 337 GLU Chi-restraints excluded: chain H residue 340 ARG Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain H residue 371 SER Chi-restraints excluded: chain H residue 475 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 354 optimal weight: 7.9990 chunk 378 optimal weight: 9.9990 chunk 301 optimal weight: 20.0000 chunk 295 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 356 optimal weight: 0.0370 chunk 344 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 HIS ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS ** H 239 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 = 0.3970 r_free = 0.3970 target = 0.184918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.167613 restraints weight = 30196.580| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 0.61 r_work: 0.3602 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 37168 Z= 0.226 Angle : 0.664 6.442 50456 Z= 0.355 Chirality : 0.046 0.169 5376 Planarity : 0.005 0.035 6600 Dihedral : 8.308 62.179 5312 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.16 % Allowed : 19.56 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: -0.36 (0.12), residues: 4520 helix: 0.56 (0.12), residues: 1792 sheet: -0.73 (0.18), residues: 712 loop : -0.67 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 132 TYR 0.028 0.002 TYR N 36 PHE 0.025 0.003 PHE B 346 TRP 0.012 0.002 TRP B 452 HIS 0.011 0.002 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.23 (37168) covalent geometry : angle 0.66424 / 0.35 (50456) hydrogen bonds : bond 0.04675 / 3.02 ( 1616) hydrogen bonds : angle 5.03973 / 3.47 ( 4440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 628 time to evaluate : 1.443 Fit side-chains REVERT: I 70 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6596 (tp) REVERT: I 72 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5879 (mm-30) REVERT: J 25 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5703 (mm-30) REVERT: J 70 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6616 (tp) REVERT: J 72 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5789 (mm-30) REVERT: K 25 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5709 (mm-30) REVERT: K 70 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6663 (tp) REVERT: K 72 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5800 (mm-30) REVERT: L 25 GLU cc_start: 0.5931 (OUTLIER) cc_final: 0.5683 (mm-30) REVERT: L 70 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6622 (tp) REVERT: L 72 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5805 (mm-30) REVERT: M 25 GLU cc_start: 0.6004 (OUTLIER) cc_final: 0.5709 (mm-30) REVERT: M 70 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6624 (tp) REVERT: M 72 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5812 (mm-30) REVERT: N 25 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.5697 (mm-30) REVERT: N 70 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6630 (tp) REVERT: N 72 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5845 (mm-30) REVERT: O 70 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6649 (tp) REVERT: O 72 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6102 (mt-10) REVERT: P 25 GLU cc_start: 0.5903 (OUTLIER) cc_final: 0.5517 (tp30) REVERT: P 70 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6641 (tp) REVERT: P 72 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5869 (mm-30) REVERT: A 179 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6779 (mp) REVERT: A 337 GLU cc_start: 0.6174 (OUTLIER) cc_final: 0.5866 (tt0) REVERT: B 179 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6778 (mp) REVERT: B 337 GLU cc_start: 0.6175 (OUTLIER) cc_final: 0.5846 (tt0) REVERT: C 179 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6780 (mp) REVERT: C 337 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5843 (tt0) REVERT: C 452 TRP cc_start: 0.4303 (t60) cc_final: 0.4099 (t60) REVERT: D 179 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6768 (mp) REVERT: D 337 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.5861 (tt0) REVERT: D 452 TRP cc_start: 0.4467 (t60) cc_final: 0.4188 (t60) REVERT: E 179 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6759 (mp) REVERT: E 337 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5868 (tt0) REVERT: F 179 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.6782 (mp) REVERT: F 337 GLU cc_start: 0.6167 (OUTLIER) cc_final: 0.5827 (tt0) REVERT: F 452 TRP cc_start: 0.4481 (t60) cc_final: 0.4197 (t60) REVERT: G 179 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6767 (mp) REVERT: G 337 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5878 (tt0) REVERT: G 452 TRP cc_start: 0.4450 (t60) cc_final: 0.4163 (t60) REVERT: H 179 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6789 (mp) REVERT: H 337 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5844 (tt0) outliers start: 156 outliers final: 94 residues processed: 697 average time/residue: 0.8497 time to fit residues: 700.4493 Evaluate side-chains 758 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 626 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain J residue 25 GLU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 25 GLU Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 72 GLU Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain P residue 25 GLU Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 80 ARG Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 359 LYS Chi-restraints excluded: chain F residue 371 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 337 GLU Chi-restraints excluded: chain H residue 340 ARG Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain H residue 371 SER Chi-restraints excluded: chain H residue 475 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 398 optimal weight: 10.0000 chunk 162 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 405 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 427 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 HIS ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS ** H 239 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 = 0.3982 r_free = 0.3982 target = 0.185985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.168530 restraints weight = 30515.238| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 0.62 r_work: 0.3613 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 37168 Z= 0.191 Angle : 0.633 6.589 50456 Z= 0.336 Chirality : 0.045 0.165 5376 Planarity : 0.005 0.038 6600 Dihedral : 8.174 61.146 5312 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.54 % Allowed : 20.82 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: -0.15 (0.12), residues: 4520 helix: 0.83 (0.12), residues: 1776 sheet: -0.64 (0.19), residues: 696 loop : -0.63 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 132 TYR 0.027 0.002 TYR N 36 PHE 0.026 0.003 PHE E 346 TRP 0.011 0.002 TRP F 67 HIS 0.011 0.002 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (37168) covalent geometry : angle 0.63350 / 0.34 (50456) hydrogen bonds : bond 0.04364 / 2.81 ( 1616) hydrogen bonds : angle 4.92226 / 3.38 ( 4440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 655 time to evaluate : 1.486 Fit side-chains REVERT: I 10 TYR cc_start: 0.7696 (m-80) cc_final: 0.7478 (m-80) REVERT: I 70 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6565 (tp) REVERT: I 72 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5863 (mm-30) REVERT: J 25 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5695 (mm-30) REVERT: J 70 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6599 (tp) REVERT: J 72 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5777 (mm-30) REVERT: K 25 GLU cc_start: 0.5954 (OUTLIER) cc_final: 0.5719 (mm-30) REVERT: K 70 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6634 (tp) REVERT: K 72 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5858 (mm-30) REVERT: L 25 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.5695 (mm-30) REVERT: L 70 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6580 (tp) REVERT: L 72 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5834 (mm-30) REVERT: M 25 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5724 (mm-30) REVERT: M 70 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6609 (tp) REVERT: M 72 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5883 (mm-30) REVERT: N 25 GLU cc_start: 0.5945 (OUTLIER) cc_final: 0.5706 (mm-30) REVERT: N 70 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6618 (tp) REVERT: N 72 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.5884 (mm-30) REVERT: O 70 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6629 (tp) REVERT: O 72 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.6077 (mt-10) REVERT: P 70 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6603 (tp) REVERT: P 72 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5874 (mm-30) REVERT: A 337 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5837 (tt0) REVERT: A 467 LYS cc_start: 0.5658 (tttp) cc_final: 0.4776 (tptt) REVERT: B 337 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5825 (tt0) REVERT: B 467 LYS cc_start: 0.5596 (tttp) cc_final: 0.4721 (tptt) REVERT: C 337 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5848 (tt0) REVERT: C 467 LYS cc_start: 0.5616 (tttp) cc_final: 0.4749 (tptt) REVERT: D 337 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.5862 (tt0) REVERT: D 467 LYS cc_start: 0.5617 (tttp) cc_final: 0.4753 (tptt) REVERT: E 337 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5842 (tt0) REVERT: E 467 LYS cc_start: 0.5594 (tttp) cc_final: 0.4716 (tptt) REVERT: F 337 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5819 (tt0) REVERT: F 467 LYS cc_start: 0.5601 (tttp) cc_final: 0.4735 (tptt) REVERT: G 337 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5855 (tt0) REVERT: G 467 LYS cc_start: 0.5682 (tttp) cc_final: 0.4811 (tptt) REVERT: H 337 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5834 (tt0) REVERT: H 467 LYS cc_start: 0.5596 (tttp) cc_final: 0.4725 (tptt) outliers start: 133 outliers final: 92 residues processed: 723 average time/residue: 0.8094 time to fit residues: 695.8308 Evaluate side-chains 746 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 625 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain J residue 25 GLU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 25 GLU Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 72 GLU Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 80 ARG Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 359 LYS Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 337 GLU Chi-restraints excluded: chain H residue 340 ARG Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain H residue 371 SER Chi-restraints excluded: chain H residue 475 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 279 optimal weight: 0.2980 chunk 183 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 325 optimal weight: 0.7980 chunk 281 optimal weight: 7.9990 chunk 390 optimal weight: 0.0050 chunk 187 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 369 optimal weight: 6.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 ASN A 227 HIS ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN B 227 HIS ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN D 227 HIS ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN E 227 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN F 227 HIS ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN G 227 HIS ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN H 227 HIS ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.189023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.171626 restraints weight = 30571.120| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 0.61 r_work: 0.3659 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 37168 Z= 0.133 Angle : 0.582 6.703 50456 Z= 0.305 Chirality : 0.043 0.159 5376 Planarity : 0.005 0.046 6600 Dihedral : 7.848 59.534 5312 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.35 % Allowed : 22.15 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: 0.15 (0.12), residues: 4520 helix: 1.24 (0.12), residues: 1784 sheet: -0.69 (0.18), residues: 776 loop : -0.54 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 132 TYR 0.022 0.002 TYR L 36 PHE 0.027 0.002 PHE D 346 TRP 0.019 0.001 TRP E 452 HIS 0.012 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (37168) covalent geometry : angle 0.58194 / 0.31 (50456) hydrogen bonds : bond 0.03728 / 2.39 ( 1616) hydrogen bonds : angle 4.67761 / 3.21 ( 4440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 690 time to evaluate : 1.489 Fit side-chains REVERT: I 72 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6071 (mm-30) REVERT: J 25 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.5505 (tp30) REVERT: J 72 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.5892 (mm-30) REVERT: K 25 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5569 (tp30) REVERT: K 72 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6040 (mm-30) REVERT: L 25 GLU cc_start: 0.5888 (OUTLIER) cc_final: 0.5501 (tp30) REVERT: L 72 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6048 (mm-30) REVERT: M 25 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5631 (mm-30) REVERT: M 72 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6097 (mm-30) REVERT: N 25 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5563 (tp30) REVERT: N 72 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6077 (mm-30) REVERT: O 25 GLU cc_start: 0.5882 (tp30) cc_final: 0.5652 (mm-30) REVERT: O 72 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.6146 (mt-10) REVERT: P 25 GLU cc_start: 0.5916 (OUTLIER) cc_final: 0.5680 (mm-30) REVERT: P 72 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6056 (mm-30) REVERT: A 132 ARG cc_start: 0.6894 (ttm110) cc_final: 0.6553 (mtt-85) REVERT: A 179 LEU cc_start: 0.7350 (mt) cc_final: 0.7113 (mm) REVERT: A 337 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5899 (tt0) REVERT: A 467 LYS cc_start: 0.5531 (tttp) cc_final: 0.4642 (tptt) REVERT: B 132 ARG cc_start: 0.6891 (ttm110) cc_final: 0.6525 (mtt-85) REVERT: B 179 LEU cc_start: 0.7351 (mt) cc_final: 0.7112 (mm) REVERT: B 337 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5909 (tt0) REVERT: B 467 LYS cc_start: 0.5551 (tttp) cc_final: 0.4675 (tptt) REVERT: C 132 ARG cc_start: 0.6892 (ttm110) cc_final: 0.6548 (mtt-85) REVERT: C 179 LEU cc_start: 0.7383 (mt) cc_final: 0.7152 (mm) REVERT: C 337 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5929 (tt0) REVERT: C 467 LYS cc_start: 0.5551 (tttp) cc_final: 0.4680 (tptt) REVERT: D 132 ARG cc_start: 0.6869 (ttm110) cc_final: 0.6541 (mtt-85) REVERT: D 179 LEU cc_start: 0.7370 (mt) cc_final: 0.7130 (mm) REVERT: D 337 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5924 (tt0) REVERT: D 467 LYS cc_start: 0.5564 (tttp) cc_final: 0.4707 (tptt) REVERT: E 132 ARG cc_start: 0.6887 (ttm110) cc_final: 0.6547 (mtt-85) REVERT: E 179 LEU cc_start: 0.7344 (mt) cc_final: 0.7107 (mm) REVERT: E 337 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5895 (tt0) REVERT: E 467 LYS cc_start: 0.5528 (tttp) cc_final: 0.4644 (tptt) REVERT: F 132 ARG cc_start: 0.6889 (ttm110) cc_final: 0.6554 (mtt-85) REVERT: F 179 LEU cc_start: 0.7367 (mt) cc_final: 0.7135 (mm) REVERT: F 337 GLU cc_start: 0.6174 (OUTLIER) cc_final: 0.5896 (tt0) REVERT: F 467 LYS cc_start: 0.5571 (tttp) cc_final: 0.4697 (tptt) REVERT: G 132 ARG cc_start: 0.6876 (ttm110) cc_final: 0.6549 (mtt-85) REVERT: G 179 LEU cc_start: 0.7369 (mt) cc_final: 0.7134 (mm) REVERT: G 337 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5909 (tt0) REVERT: G 467 LYS cc_start: 0.5588 (tttp) cc_final: 0.4728 (tptt) REVERT: H 132 ARG cc_start: 0.6913 (ttm110) cc_final: 0.6577 (mtt-85) REVERT: H 179 LEU cc_start: 0.7360 (mt) cc_final: 0.7135 (mm) REVERT: H 337 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5893 (tt0) REVERT: H 467 LYS cc_start: 0.5507 (tttp) cc_final: 0.4649 (tptt) outliers start: 88 outliers final: 42 residues processed: 737 average time/residue: 0.7749 time to fit residues: 678.8081 Evaluate side-chains 722 residues out of total 3752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 658 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain J residue 25 GLU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 25 GLU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 72 GLU Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain P residue 25 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 337 GLU Chi-restraints excluded: chain H residue 371 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 280 optimal weight: 6.9990 chunk 369 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 172 optimal weight: 0.2980 chunk 329 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 381 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 419 optimal weight: 0.9990 chunk 279 optimal weight: 0.9980 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 104 HIS K 104 HIS L 104 HIS ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 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 = 0.3980 r_free = 0.3980 target = 0.185681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.168021 restraints weight = 30314.673| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 0.64 r_work: 0.3604 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 37168 Z= 0.206 Angle : 0.653 6.399 50456 Z= 0.347 Chirality : 0.045 0.167 5376 Planarity : 0.005 0.041 6600 Dihedral : 8.064 60.810 5304 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.19 % Allowed : 22.95 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: -0.06 (0.12), residues: 4520 helix: 0.85 (0.12), residues: 1792 sheet: -0.56 (0.19), residues: 712 loop : -0.56 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 132 TYR 0.032 0.002 TYR L 36 PHE 0.026 0.003 PHE E 346 TRP 0.022 0.002 TRP E 452 HIS 0.011 0.002 HIS K 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (37168) covalent geometry : angle 0.65257 / 0.35 (50456) hydrogen bonds : bond 0.04447 / 2.87 ( 1616) hydrogen bonds : angle 4.91526 / 3.38 ( 4440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14903.17 seconds wall clock time: 255 minutes 27.98 seconds (15327.98 seconds total)