Starting phenix.real_space_refine on Mon Aug 25 17:23:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oto_70843/08_2025/9oto_70843_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oto_70843/08_2025/9oto_70843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oto_70843/08_2025/9oto_70843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oto_70843/08_2025/9oto_70843.map" model { file = "/net/cci-nas-00/data/ceres_data/9oto_70843/08_2025/9oto_70843_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oto_70843/08_2025/9oto_70843_neut.cif" } resolution = 2.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 20 5.49 5 Mg 20 5.21 5 S 220 5.16 5 C 18570 2.51 5 N 5290 2.21 5 O 5610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29730 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2944 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2944 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2944 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2944 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2944 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2944 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 348} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2944 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 348} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2944 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2944 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2944 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.21, per 1000 atoms: 0.24 Number of scatterers: 29730 At special positions: 0 Unit cell: (136.74, 135.88, 109.22, 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 220 16.00 P 20 15.00 Mg 20 11.99 O 5610 8.00 N 5290 7.00 C 18570 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: 2.16 Conformation dependent library (CDL) restraints added in 942.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6760 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 20 sheets defined 35.1% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 10 through 19 removed outlier: 4.343A pdb=" N LYS A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.626A pdb=" N LEU A 57 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 123 removed outlier: 3.734A pdb=" N ARG A 119 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 187 removed outlier: 3.975A pdb=" N VAL A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.012A pdb=" N ASP A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.839A pdb=" N ARG A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 347 through 360 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 10 through 19 removed outlier: 4.206A pdb=" N LYS B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 65 through 68 removed outlier: 3.648A pdb=" N LEU B 68 " --> pdb=" O SER B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 113 through 125 removed outlier: 3.886A pdb=" N ARG B 119 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 120 " --> pdb=" O THR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.962A pdb=" N VAL B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 233 removed outlier: 4.039A pdb=" N ASP B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 280 through 288 Processing helix chain 'B' and resid 293 through 298 removed outlier: 4.316A pdb=" N ARG B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 332 Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 10 through 19 removed outlier: 4.187A pdb=" N LYS C 14 " --> pdb=" O ASN C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.743A pdb=" N LEU C 57 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 removed outlier: 3.651A pdb=" N ARG C 119 " --> pdb=" O HIS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 172 through 187 removed outlier: 4.095A pdb=" N VAL C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 233 removed outlier: 3.965A pdb=" N ASP C 216 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 280 through 288 Processing helix chain 'C' and resid 295 through 299 Processing helix chain 'C' and resid 326 through 333 Processing helix chain 'C' and resid 347 through 360 Processing helix chain 'D' and resid 4 through 9 removed outlier: 3.663A pdb=" N LEU D 9 " --> pdb=" O SER D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 18 removed outlier: 4.249A pdb=" N LYS D 14 " --> pdb=" O ASN D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.584A pdb=" N LEU D 57 " --> pdb=" O VAL D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 68 removed outlier: 3.808A pdb=" N LEU D 68 " --> pdb=" O SER D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 113 through 124 removed outlier: 3.690A pdb=" N ARG D 119 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 128 Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.914A pdb=" N VAL D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 233 removed outlier: 3.998A pdb=" N ASP D 216 " --> pdb=" O ILE D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 280 through 288 Processing helix chain 'D' and resid 295 through 299 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 347 through 361 Processing helix chain 'E' and resid 4 through 9 removed outlier: 3.944A pdb=" N LEU E 9 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 19 removed outlier: 4.298A pdb=" N LYS E 14 " --> pdb=" O ASN E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 removed outlier: 3.639A pdb=" N LEU E 57 " --> pdb=" O VAL E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 68 removed outlier: 3.756A pdb=" N LEU E 68 " --> pdb=" O SER E 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 65 through 68' Processing helix chain 'E' and resid 113 through 123 removed outlier: 3.689A pdb=" N ARG E 119 " --> pdb=" O HIS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 172 through 187 removed outlier: 3.999A pdb=" N VAL E 176 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 233 removed outlier: 4.006A pdb=" N ASP E 216 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 266 through 278 removed outlier: 3.508A pdb=" N ALA E 273 " --> pdb=" O TYR E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 288 Processing helix chain 'E' and resid 293 through 300 removed outlier: 4.061A pdb=" N ARG E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 333 Processing helix chain 'E' and resid 347 through 361 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 10 through 19 removed outlier: 4.190A pdb=" N LYS F 14 " --> pdb=" O ASN F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 removed outlier: 3.511A pdb=" N LEU F 57 " --> pdb=" O VAL F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 123 removed outlier: 3.866A pdb=" N MET F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 128 Processing helix chain 'F' and resid 172 through 187 removed outlier: 3.913A pdb=" N VAL F 176 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 233 removed outlier: 4.047A pdb=" N ASP F 216 " --> pdb=" O ILE F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 266 through 278 Processing helix chain 'F' and resid 280 through 288 Processing helix chain 'F' and resid 293 through 298 removed outlier: 4.085A pdb=" N ARG F 298 " --> pdb=" O LEU F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 333 Processing helix chain 'F' and resid 347 through 360 Processing helix chain 'G' and resid 4 through 9 Processing helix chain 'G' and resid 10 through 19 removed outlier: 4.331A pdb=" N LYS G 14 " --> pdb=" O ASN G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 removed outlier: 3.588A pdb=" N LEU G 57 " --> pdb=" O VAL G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 124 removed outlier: 3.663A pdb=" N ARG G 119 " --> pdb=" O HIS G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 128 Processing helix chain 'G' and resid 172 through 187 removed outlier: 3.796A pdb=" N VAL G 176 " --> pdb=" O GLY G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 233 removed outlier: 3.880A pdb=" N ASP G 216 " --> pdb=" O ILE G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 264 removed outlier: 4.355A pdb=" N GLU G 264 " --> pdb=" O ALA G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 278 Processing helix chain 'G' and resid 280 through 288 Processing helix chain 'G' and resid 294 through 299 Processing helix chain 'G' and resid 326 through 333 Processing helix chain 'G' and resid 347 through 361 removed outlier: 3.692A pdb=" N LEU G 361 " --> pdb=" O ARG G 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 10 through 19 removed outlier: 4.074A pdb=" N LYS H 14 " --> pdb=" O ASN H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 removed outlier: 3.695A pdb=" N LEU H 57 " --> pdb=" O VAL H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 75 removed outlier: 3.985A pdb=" N SER H 75 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 125 removed outlier: 3.582A pdb=" N ARG H 119 " --> pdb=" O HIS H 115 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET H 123 " --> pdb=" O ARG H 119 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL H 124 " --> pdb=" O ILE H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 128 No H-bonds generated for 'chain 'H' and resid 126 through 128' Processing helix chain 'H' and resid 172 through 187 removed outlier: 3.948A pdb=" N VAL H 176 " --> pdb=" O GLY H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 233 removed outlier: 4.014A pdb=" N ASP H 216 " --> pdb=" O ILE H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 278 Processing helix chain 'H' and resid 280 through 288 Processing helix chain 'H' and resid 293 through 300 removed outlier: 4.083A pdb=" N ARG H 298 " --> pdb=" O LEU H 294 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG H 299 " --> pdb=" O ASP H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 333 Processing helix chain 'H' and resid 347 through 360 Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 10 through 19 removed outlier: 4.115A pdb=" N LYS I 14 " --> pdb=" O ASN I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 125 removed outlier: 3.696A pdb=" N MET I 123 " --> pdb=" O ARG I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 128 No H-bonds generated for 'chain 'I' and resid 126 through 128' Processing helix chain 'I' and resid 172 through 187 removed outlier: 3.894A pdb=" N VAL I 176 " --> pdb=" O GLY I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 233 removed outlier: 4.092A pdb=" N ASP I 216 " --> pdb=" O ILE I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 264 removed outlier: 3.909A pdb=" N GLU I 264 " --> pdb=" O ALA I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 278 removed outlier: 3.582A pdb=" N GLU I 272 " --> pdb=" O LYS I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 288 Processing helix chain 'I' and resid 294 through 299 Processing helix chain 'I' and resid 326 through 333 Processing helix chain 'I' and resid 347 through 361 removed outlier: 3.511A pdb=" N LEU I 361 " --> pdb=" O ARG I 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 9 Processing helix chain 'J' and resid 10 through 19 removed outlier: 4.089A pdb=" N LYS J 14 " --> pdb=" O ASN J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 67 No H-bonds generated for 'chain 'J' and resid 65 through 67' Processing helix chain 'J' and resid 113 through 125 removed outlier: 3.607A pdb=" N ARG J 119 " --> pdb=" O HIS J 115 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET J 123 " --> pdb=" O ARG J 119 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 187 removed outlier: 3.853A pdb=" N VAL J 176 " --> pdb=" O GLY J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 233 removed outlier: 3.945A pdb=" N ASP J 216 " --> pdb=" O ILE J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 263 Processing helix chain 'J' and resid 266 through 278 Processing helix chain 'J' and resid 280 through 288 Processing helix chain 'J' and resid 293 through 300 removed outlier: 3.823A pdb=" N ARG J 298 " --> pdb=" O LEU J 294 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG J 299 " --> pdb=" O ASP J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 333 Processing helix chain 'J' and resid 347 through 361 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 3.511A pdb=" N TRP A 60 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU A 79 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE A 102 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLU A 100 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN A 27 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL A 97 " --> pdb=" O GLN A 27 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N MET A 29 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N CYS A 99 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE A 31 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL A 101 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N ILE A 33 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N CYS A 42 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ALA B 195 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 193 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA B 191 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN B 205 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR B 193 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU B 203 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ALA B 195 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLN B 201 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE B 131 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 3.511A pdb=" N TRP A 60 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU A 79 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE A 102 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLU A 100 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN A 27 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL A 97 " --> pdb=" O GLN A 27 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N MET A 29 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N CYS A 99 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE A 31 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL A 101 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N ILE A 33 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N CYS A 42 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ALA B 195 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 193 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA B 191 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN B 205 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR B 193 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU B 203 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ALA B 195 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLN B 201 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE B 131 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 337 " --> pdb=" O PHE B 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 237 removed outlier: 7.054A pdb=" N GLY A 315 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 235 through 237 removed outlier: 7.154A pdb=" N MET A 133 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLY A 207 " --> pdb=" O MET A 133 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLN A 135 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLN A 205 " --> pdb=" O GLN A 135 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR A 137 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLU A 203 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU A 139 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN A 201 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLN A 201 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ALA A 195 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU A 203 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR A 193 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN A 205 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ALA A 191 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ALA A 195 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N CYS E 42 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLN E 27 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL E 97 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N MET E 29 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N CYS E 99 " --> pdb=" O MET E 29 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE E 31 " --> pdb=" O CYS E 99 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL E 101 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ILE E 33 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU E 96 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET E 84 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU E 98 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.756A pdb=" N LEU B 98 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET B 84 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 96 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN B 27 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL B 97 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET B 29 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N CYS B 99 " --> pdb=" O MET B 29 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 31 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL B 101 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ILE B 33 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N CYS B 42 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA C 195 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 193 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA C 191 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN C 205 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR C 193 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU C 203 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ALA C 195 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLN C 201 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE C 131 " --> pdb=" O PRO C 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.756A pdb=" N LEU B 98 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET B 84 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 96 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN B 27 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL B 97 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET B 29 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N CYS B 99 " --> pdb=" O MET B 29 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 31 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL B 101 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ILE B 33 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N CYS B 42 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA C 195 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 193 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA C 191 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN C 205 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR C 193 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU C 203 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ALA C 195 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLN C 201 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE C 131 " --> pdb=" O PRO C 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 63 removed outlier: 5.885A pdb=" N LEU C 79 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE C 102 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU C 100 " --> pdb=" O PRO C 81 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN C 27 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL C 97 " --> pdb=" O GLN C 27 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N MET C 29 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N CYS C 99 " --> pdb=" O MET C 29 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE C 31 " --> pdb=" O CYS C 99 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL C 101 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N ILE C 33 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N CYS C 42 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ALA D 195 " --> pdb=" O CYS C 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 193 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ALA D 191 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN D 205 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR D 193 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLU D 203 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA D 195 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N GLN D 201 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N PHE D 131 " --> pdb=" O PRO D 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 63 removed outlier: 5.885A pdb=" N LEU C 79 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE C 102 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU C 100 " --> pdb=" O PRO C 81 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN C 27 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL C 97 " --> pdb=" O GLN C 27 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N MET C 29 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N CYS C 99 " --> pdb=" O MET C 29 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE C 31 " --> pdb=" O CYS C 99 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL C 101 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N ILE C 33 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N CYS C 42 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ALA D 195 " --> pdb=" O CYS C 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 193 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ALA D 191 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN D 205 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR D 193 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLU D 203 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA D 195 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N GLN D 201 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N PHE D 131 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 337 " --> pdb=" O PHE D 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 60 through 63 removed outlier: 6.745A pdb=" N LEU D 98 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N MET D 84 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU D 96 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLN D 27 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL D 97 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N MET D 29 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N CYS D 99 " --> pdb=" O MET D 29 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE D 31 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL D 101 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ILE D 33 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N CYS D 42 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ALA E 195 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ALA E 191 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN E 205 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR E 193 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU E 203 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ALA E 195 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLN E 201 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE E 131 " --> pdb=" O PRO E 208 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 60 through 63 removed outlier: 6.745A pdb=" N LEU D 98 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N MET D 84 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU D 96 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLN D 27 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL D 97 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N MET D 29 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N CYS D 99 " --> pdb=" O MET D 29 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE D 31 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL D 101 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ILE D 33 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N CYS D 42 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ALA E 195 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ALA E 191 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN E 205 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR E 193 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU E 203 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ALA E 195 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLN E 201 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE E 131 " --> pdb=" O PRO E 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 60 through 63 removed outlier: 3.560A pdb=" N TRP F 60 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU F 98 " --> pdb=" O ALA F 82 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N MET F 84 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU F 96 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN F 27 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL F 97 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N MET F 29 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N CYS F 99 " --> pdb=" O MET F 29 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE F 31 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL F 101 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N ILE F 33 " --> pdb=" O VAL F 101 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N CYS F 42 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA G 195 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR G 193 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ALA G 191 " --> pdb=" O THR F 46 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN G 205 " --> pdb=" O ALA G 191 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR G 193 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU G 203 " --> pdb=" O THR G 193 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ALA G 195 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLN G 201 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN G 201 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU G 139 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU G 203 " --> pdb=" O TYR G 137 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TYR G 137 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLN G 205 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLN G 135 " --> pdb=" O GLN G 205 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY G 207 " --> pdb=" O MET G 133 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N MET G 133 " --> pdb=" O GLY G 207 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 60 through 63 removed outlier: 3.560A pdb=" N TRP F 60 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU F 98 " --> pdb=" O ALA F 82 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N MET F 84 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU F 96 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN F 27 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL F 97 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N MET F 29 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N CYS F 99 " --> pdb=" O MET F 29 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE F 31 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL F 101 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N ILE F 33 " --> pdb=" O VAL F 101 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N CYS F 42 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA G 195 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR G 193 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ALA G 191 " --> pdb=" O THR F 46 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN G 205 " --> pdb=" O ALA G 191 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR G 193 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU G 203 " --> pdb=" O THR G 193 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ALA G 195 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLN G 201 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN G 201 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU G 139 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU G 203 " --> pdb=" O TYR G 137 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TYR G 137 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLN G 205 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLN G 135 " --> pdb=" O GLN G 205 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY G 207 " --> pdb=" O MET G 133 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N MET G 133 " --> pdb=" O GLY G 207 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE G 337 " --> pdb=" O PHE G 256 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY G 315 " --> pdb=" O ILE G 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 235 through 237 removed outlier: 3.581A pdb=" N PHE F 337 " --> pdb=" O PHE F 256 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N GLY F 315 " --> pdb=" O ILE F 325 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 235 through 237 removed outlier: 6.011A pdb=" N PHE F 131 " --> pdb=" O PRO F 208 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET F 133 " --> pdb=" O ILE F 206 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR F 137 " --> pdb=" O TRP F 202 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLN F 201 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ALA F 195 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU F 203 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR F 193 " --> pdb=" O GLU F 203 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLN F 205 " --> pdb=" O ALA F 191 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA F 191 " --> pdb=" O THR J 46 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 193 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA F 195 " --> pdb=" O CYS J 42 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N CYS J 42 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN J 27 " --> pdb=" O LYS J 95 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL J 97 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N MET J 29 " --> pdb=" O VAL J 97 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N CYS J 99 " --> pdb=" O MET J 29 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE J 31 " --> pdb=" O CYS J 99 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL J 101 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ILE J 33 " --> pdb=" O VAL J 101 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLU J 100 " --> pdb=" O PRO J 81 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N PHE J 102 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU J 79 " --> pdb=" O PHE J 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 60 through 63 removed outlier: 6.730A pdb=" N LEU G 98 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N MET G 84 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU G 96 " --> pdb=" O MET G 84 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN G 27 " --> pdb=" O LYS G 95 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL G 97 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N MET G 29 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N CYS G 99 " --> pdb=" O MET G 29 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE G 31 " --> pdb=" O CYS G 99 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL G 101 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ILE G 33 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N CYS G 42 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALA H 195 " --> pdb=" O CYS G 42 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ALA H 191 " --> pdb=" O THR G 46 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLN H 205 " --> pdb=" O ALA H 191 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR H 193 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU H 203 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ALA H 195 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLN H 201 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE H 131 " --> pdb=" O PRO H 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 60 through 63 removed outlier: 6.730A pdb=" N LEU G 98 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N MET G 84 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU G 96 " --> pdb=" O MET G 84 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN G 27 " --> pdb=" O LYS G 95 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL G 97 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N MET G 29 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N CYS G 99 " --> pdb=" O MET G 29 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE G 31 " --> pdb=" O CYS G 99 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL G 101 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ILE G 33 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N CYS G 42 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALA H 195 " --> pdb=" O CYS G 42 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ALA H 191 " --> pdb=" O THR G 46 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLN H 205 " --> pdb=" O ALA H 191 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR H 193 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU H 203 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ALA H 195 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLN H 201 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE H 131 " --> pdb=" O PRO H 208 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS H 253 " --> pdb=" O GLU H 134 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE H 337 " --> pdb=" O PHE H 256 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY H 315 " --> pdb=" O ILE H 325 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 78 through 86 removed outlier: 6.698A pdb=" N LEU H 98 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N MET H 84 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU H 96 " --> pdb=" O MET H 84 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLN H 27 " --> pdb=" O LYS H 95 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL H 97 " --> pdb=" O GLN H 27 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N MET H 29 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N CYS H 99 " --> pdb=" O MET H 29 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE H 31 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL H 101 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ILE H 33 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N CYS H 42 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ALA I 195 " --> pdb=" O CYS H 42 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR H 44 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR I 193 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA I 191 " --> pdb=" O THR H 46 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLN I 205 " --> pdb=" O ALA I 191 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR I 193 " --> pdb=" O GLU I 203 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU I 203 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ALA I 195 " --> pdb=" O GLN I 201 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLN I 201 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE I 131 " --> pdb=" O PRO I 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 78 through 86 removed outlier: 6.698A pdb=" N LEU H 98 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N MET H 84 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU H 96 " --> pdb=" O MET H 84 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLN H 27 " --> pdb=" O LYS H 95 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL H 97 " --> pdb=" O GLN H 27 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N MET H 29 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N CYS H 99 " --> pdb=" O MET H 29 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE H 31 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL H 101 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ILE H 33 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N CYS H 42 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ALA I 195 " --> pdb=" O CYS H 42 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR H 44 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR I 193 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA I 191 " --> pdb=" O THR H 46 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLN I 205 " --> pdb=" O ALA I 191 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR I 193 " --> pdb=" O GLU I 203 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU I 203 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ALA I 195 " --> pdb=" O GLN I 201 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLN I 201 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE I 131 " --> pdb=" O PRO I 208 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS I 253 " --> pdb=" O GLU I 134 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE I 337 " --> pdb=" O PHE I 256 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY I 315 " --> pdb=" O ILE I 325 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 60 through 63 removed outlier: 3.528A pdb=" N PHE I 102 " --> pdb=" O TYR I 78 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU I 98 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N MET I 84 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU I 96 " --> pdb=" O MET I 84 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN I 27 " --> pdb=" O LYS I 95 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL I 97 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET I 29 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N CYS I 99 " --> pdb=" O MET I 29 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE I 31 " --> pdb=" O CYS I 99 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL I 101 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N ILE I 33 " --> pdb=" O VAL I 101 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N CYS I 42 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ALA J 195 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR J 193 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA J 191 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN J 205 " --> pdb=" O ALA J 191 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR J 193 " --> pdb=" O GLU J 203 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU J 203 " --> pdb=" O THR J 193 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ALA J 195 " --> pdb=" O GLN J 201 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLN J 201 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN J 201 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU J 139 " --> pdb=" O GLN J 201 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU J 203 " --> pdb=" O TYR J 137 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TYR J 137 " --> pdb=" O GLU J 203 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLN J 205 " --> pdb=" O GLN J 135 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLN J 135 " --> pdb=" O GLN J 205 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLY J 207 " --> pdb=" O MET J 133 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N MET J 133 " --> pdb=" O GLY J 207 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 60 through 63 removed outlier: 3.528A pdb=" N PHE I 102 " --> pdb=" O TYR I 78 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU I 98 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N MET I 84 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU I 96 " --> pdb=" O MET I 84 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN I 27 " --> pdb=" O LYS I 95 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL I 97 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET I 29 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N CYS I 99 " --> pdb=" O MET I 29 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE I 31 " --> pdb=" O CYS I 99 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL I 101 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N ILE I 33 " --> pdb=" O VAL I 101 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N CYS I 42 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ALA J 195 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR J 193 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA J 191 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN J 205 " --> pdb=" O ALA J 191 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR J 193 " --> pdb=" O GLU J 203 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU J 203 " --> pdb=" O THR J 193 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ALA J 195 " --> pdb=" O GLN J 201 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLN J 201 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN J 201 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU J 139 " --> pdb=" O GLN J 201 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU J 203 " --> pdb=" O TYR J 137 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TYR J 137 " --> pdb=" O GLU J 203 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLN J 205 " --> pdb=" O GLN J 135 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLN J 135 " --> pdb=" O GLN J 205 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLY J 207 " --> pdb=" O MET J 133 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N MET J 133 " --> pdb=" O GLY J 207 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLY J 315 " --> pdb=" O ILE J 325 " (cutoff:3.500A) 1326 hydrogen bonds defined for protein. 3624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.41 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9889 1.34 - 1.46: 5228 1.46 - 1.58: 15043 1.58 - 1.69: 30 1.69 - 1.81: 330 Bond restraints: 30520 Sorted by residual: bond pdb=" N SER H 19 " pdb=" CA SER H 19 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.69e+00 bond pdb=" N PHE I 369 " pdb=" CA PHE I 369 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.20e-02 6.94e+03 7.68e+00 bond pdb=" N GLN I 370 " pdb=" CA GLN I 370 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.68e+00 bond pdb=" N TYR I 371 " pdb=" CA TYR I 371 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.67e+00 bond pdb=" CA TYR I 180 " pdb=" C TYR I 180 " ideal model delta sigma weight residual 1.524 1.492 0.031 1.27e-02 6.20e+03 6.11e+00 ... (remaining 30515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 40046 1.47 - 2.93: 930 2.93 - 4.40: 278 4.40 - 5.86: 83 5.86 - 7.33: 23 Bond angle restraints: 41360 Sorted by residual: angle pdb=" O GLU I 367 " pdb=" C GLU I 367 " pdb=" N PRO I 368 " ideal model delta sigma weight residual 121.80 118.27 3.53 8.60e-01 1.35e+00 1.68e+01 angle pdb=" C TYR D 371 " pdb=" CA TYR D 371 " pdb=" CB TYR D 371 " ideal model delta sigma weight residual 115.79 111.31 4.48 1.19e+00 7.06e-01 1.42e+01 angle pdb=" CA GLU H 332 " pdb=" CB GLU H 332 " pdb=" CG GLU H 332 " ideal model delta sigma weight residual 114.10 121.43 -7.33 2.00e+00 2.50e-01 1.34e+01 angle pdb=" N MET H 18 " pdb=" CA MET H 18 " pdb=" C MET H 18 " ideal model delta sigma weight residual 113.20 108.90 4.30 1.21e+00 6.83e-01 1.27e+01 angle pdb=" C PHE I 369 " pdb=" CA PHE I 369 " pdb=" CB PHE I 369 " ideal model delta sigma weight residual 112.99 105.71 7.28 2.10e+00 2.27e-01 1.20e+01 ... (remaining 41355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.12: 16725 23.12 - 46.24: 1158 46.24 - 69.36: 184 69.36 - 92.47: 48 92.47 - 115.59: 5 Dihedral angle restraints: 18120 sinusoidal: 7500 harmonic: 10620 Sorted by residual: dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 55.59 -115.59 1 2.00e+01 2.50e-03 3.44e+01 dihedral pdb=" C5' ADP J 401 " pdb=" O5' ADP J 401 " pdb=" PA ADP J 401 " pdb=" O2A ADP J 401 " ideal model delta sinusoidal sigma weight residual -60.00 -168.98 108.99 1 2.00e+01 2.50e-03 3.18e+01 dihedral pdb=" O2A ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PA ADP F 401 " pdb=" PB ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 44.41 -104.41 1 2.00e+01 2.50e-03 3.00e+01 ... (remaining 18117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3283 0.045 - 0.090: 687 0.090 - 0.135: 203 0.135 - 0.180: 6 0.180 - 0.225: 1 Chirality restraints: 4180 Sorted by residual: chirality pdb=" CA TYR I 180 " pdb=" N TYR I 180 " pdb=" C TYR I 180 " pdb=" CB TYR I 180 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA PRO G 290 " pdb=" N PRO G 290 " pdb=" C PRO G 290 " pdb=" CB PRO G 290 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA MET H 18 " pdb=" N MET H 18 " pdb=" C MET H 18 " pdb=" CB MET H 18 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 4177 not shown) Planarity restraints: 5470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 289 " 0.081 5.00e-02 4.00e+02 1.23e-01 2.44e+01 pdb=" N PRO G 290 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO G 290 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO G 290 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 372 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C LYS A 372 " 0.043 2.00e-02 2.50e+03 pdb=" O LYS A 372 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 373 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 264 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" CD GLU C 264 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU C 264 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU C 264 " 0.013 2.00e-02 2.50e+03 ... (remaining 5467 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 96 2.41 - 3.03: 18019 3.03 - 3.66: 41540 3.66 - 4.28: 64421 4.28 - 4.90: 112303 Nonbonded interactions: 236379 Sorted by model distance: nonbonded pdb=" O3B ADP J 401 " pdb="MG MG J 402 " model vdw 1.788 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 1.824 2.170 nonbonded pdb=" O1A ADP F 401 " pdb="MG MG F 403 " model vdw 1.838 2.170 nonbonded pdb=" O3B ADP H 401 " pdb="MG MG H 402 " model vdw 1.846 2.170 nonbonded pdb=" O2A ADP I 401 " pdb="MG MG I 402 " model vdw 1.864 2.170 ... (remaining 236374 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' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.690 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 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 : 0.003 0.036 30520 Z= 0.143 Angle : 0.630 7.331 41360 Z= 0.311 Chirality : 0.041 0.225 4180 Planarity : 0.004 0.123 5470 Dihedral : 15.860 115.594 11360 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.15 % Allowed : 11.92 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.14), residues: 3700 helix: 1.96 (0.16), residues: 1050 sheet: -0.56 (0.18), residues: 810 loop : -0.67 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 107 TYR 0.018 0.001 TYR F 269 PHE 0.010 0.001 PHE G 204 TRP 0.010 0.001 TRP C 60 HIS 0.003 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00293 (30520) covalent geometry : angle 0.62964 (41360) hydrogen bonds : bond 0.18384 ( 1126) hydrogen bonds : angle 6.59146 ( 3624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 THR cc_start: 0.7181 (m) cc_final: 0.6981 (t) REVERT: H 369 PHE cc_start: 0.7848 (t80) cc_final: 0.7278 (t80) outliers start: 36 outliers final: 27 residues processed: 250 average time/residue: 0.6927 time to fit residues: 199.1649 Evaluate side-chains 232 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 90 ARG Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain H residue 356 ILE Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 209 CYS Chi-restraints excluded: chain I residue 372 LYS Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 217 HIS E 152 ASN F 135 GLN G 74 ASN G 158 GLN H 246 ASN J 253 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.104512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.074231 restraints weight = 50950.860| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.47 r_work: 0.2890 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 30520 Z= 0.231 Angle : 0.766 12.051 41360 Z= 0.386 Chirality : 0.050 0.222 4180 Planarity : 0.005 0.077 5470 Dihedral : 8.611 124.500 4277 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.21 % Allowed : 11.47 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.14), residues: 3700 helix: 1.73 (0.16), residues: 1050 sheet: -0.17 (0.18), residues: 730 loop : -0.90 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 107 TYR 0.013 0.002 TYR D 78 PHE 0.016 0.002 PHE G 204 TRP 0.012 0.001 TRP C 60 HIS 0.005 0.001 HIS J 284 Details of bonding type rmsd covalent geometry : bond 0.00546 (30520) covalent geometry : angle 0.76558 (41360) hydrogen bonds : bond 0.07880 ( 1126) hydrogen bonds : angle 5.24990 ( 3624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 224 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7711 (p0) REVERT: A 275 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: A 332 GLU cc_start: 0.8794 (tt0) cc_final: 0.8524 (tp30) REVERT: E 77 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8468 (mmm) REVERT: E 121 MET cc_start: 0.8663 (mmm) cc_final: 0.8319 (mmt) REVERT: E 169 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8064 (mtm180) REVERT: F 361 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7643 (pp) REVERT: F 369 PHE cc_start: 0.8410 (t80) cc_final: 0.8118 (t80) REVERT: F 373 ASN cc_start: 0.7691 (t0) cc_final: 0.7436 (t0) REVERT: G 305 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7851 (mm-30) REVERT: G 366 ASP cc_start: 0.8518 (t0) cc_final: 0.8195 (t0) REVERT: H 369 PHE cc_start: 0.7929 (t80) cc_final: 0.7108 (t80) REVERT: I 263 GLU cc_start: 0.8648 (pt0) cc_final: 0.8291 (pt0) REVERT: I 265 ASN cc_start: 0.7635 (t0) cc_final: 0.7377 (t0) REVERT: J 275 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7709 (mm-30) outliers start: 69 outliers final: 30 residues processed: 280 average time/residue: 0.6457 time to fit residues: 209.3799 Evaluate side-chains 247 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 90 ARG Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 356 ILE Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 209 CYS Chi-restraints excluded: chain I residue 372 LYS Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 127 GLN Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 356 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 348 optimal weight: 0.0000 chunk 286 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 217 optimal weight: 7.9990 chunk 262 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 338 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 HIS D 373 ASN E 152 ASN F 22 GLN F 94 ASN H 201 GLN H 246 ASN J 179 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.108154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078183 restraints weight = 50809.106| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.46 r_work: 0.2968 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30520 Z= 0.122 Angle : 0.640 15.497 41360 Z= 0.310 Chirality : 0.044 0.173 4180 Planarity : 0.004 0.055 5470 Dihedral : 7.749 103.352 4261 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.57 % Allowed : 12.12 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.14), residues: 3700 helix: 2.06 (0.16), residues: 1050 sheet: -0.34 (0.18), residues: 810 loop : -0.81 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 107 TYR 0.016 0.001 TYR F 104 PHE 0.011 0.001 PHE J 337 TRP 0.023 0.001 TRP J 130 HIS 0.003 0.000 HIS G 217 Details of bonding type rmsd covalent geometry : bond 0.00256 (30520) covalent geometry : angle 0.63978 (41360) hydrogen bonds : bond 0.04833 ( 1126) hydrogen bonds : angle 4.69241 ( 3624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7919 (mm-30) REVERT: A 332 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8464 (tp30) REVERT: A 366 ASP cc_start: 0.8408 (t0) cc_final: 0.8107 (t0) REVERT: E 121 MET cc_start: 0.8477 (mmm) cc_final: 0.8166 (mmt) REVERT: E 169 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8047 (mtm180) REVERT: E 265 ASN cc_start: 0.7917 (t0) cc_final: 0.7690 (t0) REVERT: F 79 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8651 (pp) REVERT: F 361 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7676 (pp) REVERT: F 369 PHE cc_start: 0.8404 (t80) cc_final: 0.7921 (t80) REVERT: G 305 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7772 (mm-30) REVERT: G 366 ASP cc_start: 0.8617 (t0) cc_final: 0.8228 (t0) REVERT: H 227 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.7653 (mmm160) REVERT: H 369 PHE cc_start: 0.7923 (t80) cc_final: 0.7079 (t80) REVERT: I 263 GLU cc_start: 0.8657 (pt0) cc_final: 0.8314 (pt0) REVERT: J 38 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: J 275 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7712 (mm-30) outliers start: 49 outliers final: 18 residues processed: 271 average time/residue: 0.6896 time to fit residues: 215.0625 Evaluate side-chains 234 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 356 ILE Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 209 CYS Chi-restraints excluded: chain I residue 372 LYS Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 127 GLN Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 141 optimal weight: 0.0020 chunk 185 optimal weight: 8.9990 chunk 269 optimal weight: 0.0370 chunk 311 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 333 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 292 optimal weight: 5.9990 chunk 314 optimal weight: 3.9990 overall best weight: 0.9468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN D 373 ASN E 152 ASN H 246 ASN I 373 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.107307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.077266 restraints weight = 50650.154| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.45 r_work: 0.2950 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30520 Z= 0.133 Angle : 0.651 14.728 41360 Z= 0.314 Chirality : 0.044 0.174 4180 Planarity : 0.004 0.055 5470 Dihedral : 7.339 103.535 4244 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.73 % Allowed : 12.47 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.14), residues: 3700 helix: 2.09 (0.16), residues: 1050 sheet: -0.25 (0.18), residues: 810 loop : -0.80 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 107 TYR 0.014 0.001 TYR F 104 PHE 0.012 0.001 PHE G 204 TRP 0.009 0.001 TRP C 60 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00288 (30520) covalent geometry : angle 0.65078 (41360) hydrogen bonds : bond 0.05356 ( 1126) hydrogen bonds : angle 4.65141 ( 3624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 215 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: A 332 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8347 (tp30) REVERT: A 366 ASP cc_start: 0.8467 (t0) cc_final: 0.8100 (t0) REVERT: D 175 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9033 (mp) REVERT: E 121 MET cc_start: 0.8485 (mmm) cc_final: 0.8178 (mmt) REVERT: E 169 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8044 (mtm180) REVERT: E 175 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8677 (mt) REVERT: E 265 ASN cc_start: 0.7838 (t0) cc_final: 0.7508 (t0) REVERT: E 311 ASP cc_start: 0.5376 (OUTLIER) cc_final: 0.4384 (p0) REVERT: F 79 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8713 (pp) REVERT: F 361 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7626 (pp) REVERT: F 369 PHE cc_start: 0.8352 (t80) cc_final: 0.7664 (t80) REVERT: G 68 LEU cc_start: 0.9443 (tp) cc_final: 0.9177 (tt) REVERT: G 305 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7745 (mm-30) REVERT: G 366 ASP cc_start: 0.8679 (t0) cc_final: 0.8404 (t0) REVERT: H 227 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.7680 (mmm160) REVERT: H 369 PHE cc_start: 0.7914 (t80) cc_final: 0.7033 (t80) REVERT: I 263 GLU cc_start: 0.8632 (pt0) cc_final: 0.8266 (pt0) REVERT: J 275 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7717 (mm-30) REVERT: J 332 GLU cc_start: 0.8343 (tp30) cc_final: 0.8125 (tp30) outliers start: 54 outliers final: 27 residues processed: 259 average time/residue: 0.6774 time to fit residues: 202.7753 Evaluate side-chains 240 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 356 ILE Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 209 CYS Chi-restraints excluded: chain I residue 366 ASP Chi-restraints excluded: chain I residue 372 LYS Chi-restraints excluded: chain I residue 373 ASN Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 127 GLN Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 312 optimal weight: 3.9990 chunk 331 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 353 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 344 optimal weight: 0.9980 chunk 291 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 373 ASN E 152 ASN H 152 ASN H 246 ASN ** J 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.106848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.076586 restraints weight = 50607.732| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.47 r_work: 0.2937 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30520 Z= 0.150 Angle : 0.670 15.126 41360 Z= 0.325 Chirality : 0.045 0.181 4180 Planarity : 0.004 0.056 5470 Dihedral : 7.276 104.597 4244 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.15 % Allowed : 12.28 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.14), residues: 3700 helix: 2.06 (0.16), residues: 1050 sheet: -0.25 (0.18), residues: 810 loop : -0.80 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 107 TYR 0.014 0.001 TYR F 104 PHE 0.014 0.001 PHE G 204 TRP 0.012 0.001 TRP C 60 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00334 (30520) covalent geometry : angle 0.67032 (41360) hydrogen bonds : bond 0.05793 ( 1126) hydrogen bonds : angle 4.70332 ( 3624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 216 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7919 (mm-30) REVERT: A 332 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8378 (tp30) REVERT: A 366 ASP cc_start: 0.8465 (t0) cc_final: 0.8084 (t0) REVERT: D 175 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9045 (mp) REVERT: E 77 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8391 (mmm) REVERT: E 121 MET cc_start: 0.8547 (mmm) cc_final: 0.8265 (mmt) REVERT: E 169 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8039 (mtm180) REVERT: E 175 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8715 (mt) REVERT: E 265 ASN cc_start: 0.7817 (t0) cc_final: 0.7441 (t0) REVERT: E 311 ASP cc_start: 0.5384 (OUTLIER) cc_final: 0.4375 (p0) REVERT: F 54 VAL cc_start: 0.9293 (OUTLIER) cc_final: 0.9082 (p) REVERT: F 79 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8741 (pp) REVERT: F 361 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7563 (pp) REVERT: F 369 PHE cc_start: 0.8324 (t80) cc_final: 0.7555 (t80) REVERT: G 305 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7710 (mm-30) REVERT: G 366 ASP cc_start: 0.8729 (t0) cc_final: 0.8451 (t0) REVERT: H 227 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.7694 (mmm160) REVERT: H 332 GLU cc_start: 0.8536 (tp30) cc_final: 0.8325 (tp30) REVERT: H 369 PHE cc_start: 0.7951 (t80) cc_final: 0.7155 (t80) REVERT: I 263 GLU cc_start: 0.8617 (pt0) cc_final: 0.8271 (pt0) REVERT: J 275 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7687 (mm-30) REVERT: J 332 GLU cc_start: 0.8419 (tp30) cc_final: 0.8199 (tp30) outliers start: 67 outliers final: 30 residues processed: 270 average time/residue: 0.6629 time to fit residues: 207.5664 Evaluate side-chains 246 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 356 ILE Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 366 ASP Chi-restraints excluded: chain I residue 372 LYS Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 127 GLN Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 322 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 144 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 247 optimal weight: 8.9990 chunk 243 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 351 optimal weight: 3.9990 chunk 330 optimal weight: 0.0970 chunk 348 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 ASN D 201 GLN D 373 ASN E 152 ASN H 246 ASN ** J 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.108504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.078646 restraints weight = 50549.695| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.45 r_work: 0.2979 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30520 Z= 0.114 Angle : 0.621 15.109 41360 Z= 0.295 Chirality : 0.043 0.165 4180 Planarity : 0.004 0.056 5470 Dihedral : 6.712 100.373 4243 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.83 % Allowed : 12.92 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.14), residues: 3700 helix: 2.18 (0.16), residues: 1050 sheet: -0.23 (0.18), residues: 810 loop : -0.74 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 107 TYR 0.017 0.001 TYR F 104 PHE 0.011 0.001 PHE J 337 TRP 0.013 0.001 TRP C 60 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00240 (30520) covalent geometry : angle 0.62079 (41360) hydrogen bonds : bond 0.04448 ( 1126) hydrogen bonds : angle 4.46925 ( 3624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 222 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7973 (mm-30) REVERT: A 332 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8374 (tp30) REVERT: A 366 ASP cc_start: 0.8535 (t0) cc_final: 0.8102 (t0) REVERT: B 38 GLU cc_start: 0.8418 (pt0) cc_final: 0.8139 (pm20) REVERT: C 127 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7088 (mp10) REVERT: D 175 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8938 (mp) REVERT: E 121 MET cc_start: 0.8483 (mmm) cc_final: 0.8159 (mmt) REVERT: E 169 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8023 (mtm180) REVERT: E 175 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8621 (mt) REVERT: E 227 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7973 (mmm160) REVERT: E 265 ASN cc_start: 0.7753 (t0) cc_final: 0.7331 (t0) REVERT: F 275 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8288 (mm-30) REVERT: F 331 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8598 (mt0) REVERT: F 361 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7538 (pp) REVERT: F 369 PHE cc_start: 0.8326 (t80) cc_final: 0.7553 (t80) REVERT: G 68 LEU cc_start: 0.9420 (tp) cc_final: 0.9165 (tt) REVERT: G 305 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7735 (mm-30) REVERT: G 366 ASP cc_start: 0.8736 (t0) cc_final: 0.8443 (t0) REVERT: H 123 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8043 (mtp) REVERT: H 308 ASN cc_start: 0.7354 (OUTLIER) cc_final: 0.7130 (t0) REVERT: H 369 PHE cc_start: 0.8042 (t80) cc_final: 0.7284 (t80) REVERT: I 263 GLU cc_start: 0.8588 (pt0) cc_final: 0.8250 (pt0) REVERT: J 38 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8507 (mp0) REVERT: J 275 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7708 (mm-30) REVERT: J 332 GLU cc_start: 0.8460 (tp30) cc_final: 0.8226 (tp30) outliers start: 57 outliers final: 28 residues processed: 269 average time/residue: 0.6900 time to fit residues: 214.6909 Evaluate side-chains 249 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 373 ASN Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 308 ASN Chi-restraints excluded: chain H residue 356 ILE Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 372 LYS Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 127 GLN Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 255 optimal weight: 7.9990 chunk 199 optimal weight: 0.8980 chunk 357 optimal weight: 5.9990 chunk 30 optimal weight: 0.0370 chunk 151 optimal weight: 0.6980 chunk 331 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 330 optimal weight: 3.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 373 ASN E 152 ASN H 246 ASN ** J 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.108041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.077853 restraints weight = 50392.320| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.47 r_work: 0.2962 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30520 Z= 0.128 Angle : 0.641 15.268 41360 Z= 0.307 Chirality : 0.044 0.170 4180 Planarity : 0.004 0.056 5470 Dihedral : 6.658 101.305 4243 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.79 % Allowed : 13.43 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.14), residues: 3700 helix: 2.17 (0.16), residues: 1050 sheet: -0.22 (0.18), residues: 810 loop : -0.74 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 107 TYR 0.016 0.001 TYR F 104 PHE 0.012 0.001 PHE G 204 TRP 0.013 0.001 TRP C 60 HIS 0.003 0.000 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00280 (30520) covalent geometry : angle 0.64121 (41360) hydrogen bonds : bond 0.05039 ( 1126) hydrogen bonds : angle 4.50840 ( 3624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 214 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7919 (mm-30) REVERT: A 332 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8370 (tp30) REVERT: A 366 ASP cc_start: 0.8526 (t0) cc_final: 0.8071 (t0) REVERT: B 38 GLU cc_start: 0.8506 (pt0) cc_final: 0.8198 (pm20) REVERT: C 127 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: D 175 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9020 (mp) REVERT: E 77 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8359 (mmm) REVERT: E 121 MET cc_start: 0.8497 (mmm) cc_final: 0.8179 (mmt) REVERT: E 169 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8024 (mtm180) REVERT: E 175 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8672 (mt) REVERT: E 227 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.7998 (mmm160) REVERT: E 265 ASN cc_start: 0.7790 (t0) cc_final: 0.7341 (t0) REVERT: E 311 ASP cc_start: 0.5510 (OUTLIER) cc_final: 0.4843 (p0) REVERT: F 275 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8323 (mm-30) REVERT: F 361 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7503 (pp) REVERT: F 369 PHE cc_start: 0.8311 (t80) cc_final: 0.7515 (t80) REVERT: G 68 LEU cc_start: 0.9400 (tp) cc_final: 0.9139 (tt) REVERT: G 305 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7737 (mm-30) REVERT: G 366 ASP cc_start: 0.8771 (t0) cc_final: 0.8269 (t0) REVERT: G 367 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8726 (mm-30) REVERT: H 123 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8126 (mtp) REVERT: H 227 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.7595 (mmm160) REVERT: H 308 ASN cc_start: 0.7329 (OUTLIER) cc_final: 0.7101 (t0) REVERT: H 332 GLU cc_start: 0.8494 (tp30) cc_final: 0.8284 (tp30) REVERT: H 369 PHE cc_start: 0.8064 (t80) cc_final: 0.7321 (t80) REVERT: I 113 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8392 (mt) REVERT: I 263 GLU cc_start: 0.8554 (pt0) cc_final: 0.8213 (pt0) REVERT: J 38 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: J 275 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7712 (mm-30) REVERT: J 332 GLU cc_start: 0.8447 (tp30) cc_final: 0.8200 (tp30) outliers start: 56 outliers final: 31 residues processed: 260 average time/residue: 0.6576 time to fit residues: 197.7846 Evaluate side-chains 258 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 373 ASN Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 308 ASN Chi-restraints excluded: chain H residue 356 ILE Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 366 ASP Chi-restraints excluded: chain I residue 372 LYS Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 127 GLN Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 356 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 264 optimal weight: 0.0570 chunk 102 optimal weight: 0.4980 chunk 171 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 282 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 134 optimal weight: 0.3980 chunk 56 optimal weight: 0.0370 chunk 84 optimal weight: 1.9990 chunk 266 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 HIS D 373 ASN E 152 ASN F 281 HIS H 246 ASN ** J 128 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 = 0.3661 r_free = 0.3661 target = 0.110044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.080354 restraints weight = 50888.154| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.46 r_work: 0.3014 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30520 Z= 0.104 Angle : 0.604 15.272 41360 Z= 0.285 Chirality : 0.042 0.156 4180 Planarity : 0.004 0.060 5470 Dihedral : 6.139 96.231 4243 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.47 % Allowed : 13.91 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.14), residues: 3700 helix: 2.30 (0.16), residues: 1050 sheet: -0.17 (0.18), residues: 800 loop : -0.69 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 107 TYR 0.018 0.001 TYR F 104 PHE 0.010 0.001 PHE J 337 TRP 0.015 0.001 TRP C 60 HIS 0.002 0.000 HIS G 217 Details of bonding type rmsd covalent geometry : bond 0.00218 (30520) covalent geometry : angle 0.60415 (41360) hydrogen bonds : bond 0.03750 ( 1126) hydrogen bonds : angle 4.28099 ( 3624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8146 (pm20) cc_final: 0.7918 (mm-30) REVERT: A 121 MET cc_start: 0.9149 (mmt) cc_final: 0.8894 (mmt) REVERT: A 275 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8005 (mm-30) REVERT: A 332 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8317 (tp30) REVERT: A 366 ASP cc_start: 0.8539 (t0) cc_final: 0.8064 (t0) REVERT: C 127 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7055 (mp10) REVERT: D 107 ARG cc_start: 0.8256 (ptp-110) cc_final: 0.8055 (ptp90) REVERT: E 169 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8053 (mtm180) REVERT: E 175 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8557 (mt) REVERT: E 227 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7774 (mmm160) REVERT: E 265 ASN cc_start: 0.7777 (t0) cc_final: 0.7264 (t0) REVERT: E 311 ASP cc_start: 0.5771 (OUTLIER) cc_final: 0.5161 (p0) REVERT: F 275 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8331 (mm-30) REVERT: F 361 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7507 (pp) REVERT: F 369 PHE cc_start: 0.8259 (t80) cc_final: 0.7457 (t80) REVERT: G 68 LEU cc_start: 0.9406 (tp) cc_final: 0.9158 (tt) REVERT: G 305 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7749 (mm-30) REVERT: G 366 ASP cc_start: 0.8774 (t0) cc_final: 0.8224 (t0) REVERT: G 367 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8655 (mm-30) REVERT: H 227 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.7582 (mmm160) REVERT: H 308 ASN cc_start: 0.7328 (OUTLIER) cc_final: 0.7092 (t0) REVERT: H 369 PHE cc_start: 0.8052 (t80) cc_final: 0.7458 (t80) REVERT: I 263 GLU cc_start: 0.8537 (pt0) cc_final: 0.8219 (pt0) REVERT: I 265 ASN cc_start: 0.8334 (m-40) cc_final: 0.7748 (t0) REVERT: J 38 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8510 (mp0) REVERT: J 275 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7715 (mm-30) REVERT: J 332 GLU cc_start: 0.8441 (tp30) cc_final: 0.8190 (tp30) outliers start: 46 outliers final: 24 residues processed: 256 average time/residue: 0.6784 time to fit residues: 199.7448 Evaluate side-chains 245 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 308 ASN Chi-restraints excluded: chain H residue 356 ILE Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 372 LYS Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 127 GLN Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 200 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 345 optimal weight: 0.7980 chunk 249 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 310 optimal weight: 0.2980 chunk 99 optimal weight: 6.9990 chunk 369 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 373 ASN E 152 ASN H 246 ASN ** J 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.109265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.079449 restraints weight = 50572.293| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.45 r_work: 0.2996 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 30520 Z= 0.111 Angle : 0.617 15.127 41360 Z= 0.293 Chirality : 0.042 0.159 4180 Planarity : 0.004 0.063 5470 Dihedral : 6.068 95.369 4242 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.47 % Allowed : 14.17 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.14), residues: 3700 helix: 2.31 (0.16), residues: 1050 sheet: -0.15 (0.18), residues: 800 loop : -0.67 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 107 TYR 0.017 0.001 TYR F 104 PHE 0.012 0.001 PHE I 369 TRP 0.006 0.001 TRP I 32 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00239 (30520) covalent geometry : angle 0.61693 (41360) hydrogen bonds : bond 0.04255 ( 1126) hydrogen bonds : angle 4.28962 ( 3624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7760 (mmm160) REVERT: A 275 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7982 (mm-30) REVERT: A 332 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8350 (tp30) REVERT: A 366 ASP cc_start: 0.8558 (t0) cc_final: 0.8044 (t0) REVERT: B 38 GLU cc_start: 0.8383 (pt0) cc_final: 0.8135 (pm20) REVERT: C 127 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7035 (mp10) REVERT: D 107 ARG cc_start: 0.8271 (ptp-110) cc_final: 0.8057 (ptp90) REVERT: E 169 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8024 (mtm180) REVERT: E 175 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8663 (mt) REVERT: E 227 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.7786 (mmm160) REVERT: E 265 ASN cc_start: 0.7870 (t0) cc_final: 0.7321 (t0) REVERT: E 311 ASP cc_start: 0.5904 (OUTLIER) cc_final: 0.5291 (p0) REVERT: F 361 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7485 (pp) REVERT: F 369 PHE cc_start: 0.8303 (t80) cc_final: 0.7471 (t80) REVERT: G 68 LEU cc_start: 0.9415 (tp) cc_final: 0.9166 (tt) REVERT: G 305 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7750 (mm-30) REVERT: G 366 ASP cc_start: 0.8807 (t0) cc_final: 0.8320 (t0) REVERT: G 367 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8759 (mm-30) REVERT: H 2 THR cc_start: 0.7483 (m) cc_final: 0.7200 (t) REVERT: H 227 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.7595 (mmm160) REVERT: H 308 ASN cc_start: 0.7263 (OUTLIER) cc_final: 0.7039 (t0) REVERT: H 369 PHE cc_start: 0.8040 (t80) cc_final: 0.7432 (t80) REVERT: I 263 GLU cc_start: 0.8568 (pt0) cc_final: 0.8254 (pt0) REVERT: I 265 ASN cc_start: 0.8405 (m-40) cc_final: 0.7692 (t0) REVERT: J 38 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: J 275 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7715 (mm-30) REVERT: J 332 GLU cc_start: 0.8478 (tp30) cc_final: 0.8204 (tp30) outliers start: 46 outliers final: 25 residues processed: 250 average time/residue: 0.6603 time to fit residues: 189.0220 Evaluate side-chains 241 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain C residue 60 TRP Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 308 ASN Chi-restraints excluded: chain H residue 356 ILE Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 372 LYS Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 127 GLN Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 151 optimal weight: 2.9990 chunk 284 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 0.0570 chunk 5 optimal weight: 0.6980 chunk 279 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 276 optimal weight: 1.9990 chunk 156 optimal weight: 0.0770 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 373 ASN H 246 ASN ** J 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.109445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.079632 restraints weight = 50581.843| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.48 r_work: 0.2999 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30520 Z= 0.110 Angle : 0.615 15.085 41360 Z= 0.292 Chirality : 0.042 0.158 4180 Planarity : 0.004 0.065 5470 Dihedral : 5.966 93.844 4242 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.31 % Allowed : 14.36 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.14), residues: 3700 helix: 2.30 (0.16), residues: 1050 sheet: -0.15 (0.18), residues: 800 loop : -0.64 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG H 107 TYR 0.017 0.001 TYR F 104 PHE 0.026 0.001 PHE I 369 TRP 0.016 0.001 TRP C 60 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00235 (30520) covalent geometry : angle 0.61531 (41360) hydrogen bonds : bond 0.04139 ( 1126) hydrogen bonds : angle 4.27509 ( 3624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7759 (mmm160) REVERT: A 275 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7996 (mm-30) REVERT: A 332 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8452 (tp30) REVERT: A 366 ASP cc_start: 0.8563 (t0) cc_final: 0.8044 (t0) REVERT: B 38 GLU cc_start: 0.8389 (pt0) cc_final: 0.8139 (pm20) REVERT: C 127 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7090 (mp10) REVERT: D 107 ARG cc_start: 0.8248 (ptp-110) cc_final: 0.8019 (ptp90) REVERT: D 175 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.8946 (mp) REVERT: E 169 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8018 (mtm180) REVERT: E 175 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8644 (mt) REVERT: E 227 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7932 (mmm160) REVERT: E 265 ASN cc_start: 0.7912 (t0) cc_final: 0.7343 (t0) REVERT: E 311 ASP cc_start: 0.5905 (OUTLIER) cc_final: 0.5282 (p0) REVERT: F 50 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: F 291 LYS cc_start: 0.7880 (mmmt) cc_final: 0.7676 (mptt) REVERT: F 361 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7483 (pp) REVERT: F 369 PHE cc_start: 0.8295 (t80) cc_final: 0.7455 (t80) REVERT: G 68 LEU cc_start: 0.9411 (tp) cc_final: 0.9177 (tt) REVERT: G 305 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7745 (mm-30) REVERT: G 366 ASP cc_start: 0.8816 (t0) cc_final: 0.8540 (t0) REVERT: H 2 THR cc_start: 0.7494 (m) cc_final: 0.7217 (t) REVERT: H 227 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.7601 (mmm160) REVERT: H 308 ASN cc_start: 0.7245 (OUTLIER) cc_final: 0.7034 (t0) REVERT: H 369 PHE cc_start: 0.8043 (t80) cc_final: 0.7432 (t80) REVERT: I 263 GLU cc_start: 0.8559 (pt0) cc_final: 0.8237 (pt0) REVERT: I 265 ASN cc_start: 0.8439 (m-40) cc_final: 0.7700 (t0) REVERT: J 38 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8531 (mp0) REVERT: J 275 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7702 (mm-30) REVERT: J 332 GLU cc_start: 0.8494 (tp30) cc_final: 0.8212 (tp30) outliers start: 41 outliers final: 22 residues processed: 245 average time/residue: 0.6412 time to fit residues: 179.9119 Evaluate side-chains 242 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 308 ASN Chi-restraints excluded: chain H residue 356 ILE Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 372 LYS Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 310 optimal weight: 0.8980 chunk 113 optimal weight: 0.0370 chunk 333 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 145 optimal weight: 0.0770 chunk 265 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 278 optimal weight: 0.0570 overall best weight: 0.2312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 373 ASN E 152 ASN G 8 HIS G 179 HIS H 246 ASN ** J 128 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 = 0.3691 r_free = 0.3691 target = 0.111888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082436 restraints weight = 50718.367| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.45 r_work: 0.3057 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 30520 Z= 0.099 Angle : 0.592 14.948 41360 Z= 0.277 Chirality : 0.041 0.158 4180 Planarity : 0.004 0.065 5470 Dihedral : 5.648 87.546 4242 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.19 % Allowed : 14.58 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.14), residues: 3700 helix: 2.52 (0.16), residues: 1020 sheet: 0.18 (0.18), residues: 780 loop : -0.65 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 107 TYR 0.016 0.001 TYR G 104 PHE 0.022 0.001 PHE I 369 TRP 0.009 0.001 TRP C 60 HIS 0.002 0.000 HIS G 217 Details of bonding type rmsd covalent geometry : bond 0.00212 (30520) covalent geometry : angle 0.59237 (41360) hydrogen bonds : bond 0.03178 ( 1126) hydrogen bonds : angle 4.08606 ( 3624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13109.39 seconds wall clock time: 222 minutes 48.06 seconds (13368.06 seconds total)