Starting phenix.real_space_refine on Sat Feb 7 14:01:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cro_45873/02_2026/9cro_45873_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cro_45873/02_2026/9cro_45873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cro_45873/02_2026/9cro_45873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cro_45873/02_2026/9cro_45873.map" model { file = "/net/cci-nas-00/data/ceres_data/9cro_45873/02_2026/9cro_45873_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cro_45873/02_2026/9cro_45873_trim.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 524 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 43 5.49 5 S 79 5.16 5 C 15974 2.51 5 N 4226 2.21 5 O 4956 1.98 5 H 7191 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32469 Number of models: 1 Model: "" Number of chains: 21 Chain: "J" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 977 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Chain: "I" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 977 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Chain: "K" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 977 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Chain: "L" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 977 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Chain: "M" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 977 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Chain: "N" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 1 Chain: "B" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "C" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "A" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "H" Number of atoms: 1666 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1661 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 196} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 207, 1661 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 196} Chain breaks: 3 bond proxies already assigned to first conformer: 1695 Chain: "S" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 926 Classifications: {'RNA': 44} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 15, 'rna3p_pur': 12, 'rna3p_pyr': 8} Link IDs: {'rna2p': 23, 'rna3p': 20} Chain: "E" Number of atoms: 4959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4959 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "F" Number of atoms: 4959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4959 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "G" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4282 Classifications: {'peptide': 272} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain breaks: 4 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'TRS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.53, per 1000 atoms: 0.20 Number of scatterers: 32469 At special positions: 0 Unit cell: (151.94, 143.42, 183.18, 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 79 16.00 P 43 15.00 O 4956 8.00 N 4226 7.00 C 15974 6.00 H 7191 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5798 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 33 sheets defined 43.2% alpha, 16.3% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'J' and resid 6 through 26 Processing helix chain 'J' and resid 28 through 36 Processing helix chain 'J' and resid 39 through 60 Processing helix chain 'J' and resid 102 through 116 Processing helix chain 'J' and resid 117 through 142 removed outlier: 3.708A pdb=" N ARG J 121 " --> pdb=" O VAL J 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 26 Processing helix chain 'I' and resid 28 through 36 Processing helix chain 'I' and resid 39 through 60 Processing helix chain 'I' and resid 102 through 116 Processing helix chain 'I' and resid 117 through 141 removed outlier: 3.709A pdb=" N ARG I 121 " --> pdb=" O VAL I 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 26 Processing helix chain 'K' and resid 28 through 36 Processing helix chain 'K' and resid 39 through 60 Processing helix chain 'K' and resid 102 through 116 Processing helix chain 'K' and resid 117 through 142 removed outlier: 3.719A pdb=" N ARG K 121 " --> pdb=" O VAL K 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 26 Processing helix chain 'L' and resid 28 through 36 Processing helix chain 'L' and resid 39 through 60 Processing helix chain 'L' and resid 102 through 116 Processing helix chain 'L' and resid 117 through 142 removed outlier: 3.717A pdb=" N ARG L 121 " --> pdb=" O VAL L 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 26 Processing helix chain 'M' and resid 28 through 36 Processing helix chain 'M' and resid 39 through 60 Processing helix chain 'M' and resid 102 through 116 Processing helix chain 'M' and resid 117 through 142 removed outlier: 3.724A pdb=" N ARG M 121 " --> pdb=" O VAL M 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 26 Processing helix chain 'N' and resid 28 through 37 Processing helix chain 'N' and resid 39 through 60 Processing helix chain 'N' and resid 102 through 116 Processing helix chain 'N' and resid 117 through 138 removed outlier: 3.660A pdb=" N ARG N 121 " --> pdb=" O VAL N 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 69 removed outlier: 4.291A pdb=" N LEU B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.927A pdb=" N GLN B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.554A pdb=" N LEU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.549A pdb=" N ASP B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 195 removed outlier: 3.634A pdb=" N ILE B 195 " --> pdb=" O GLU B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 192 through 195' Processing helix chain 'B' and resid 207 through 225 removed outlier: 3.638A pdb=" N LEU B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 4.310A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.549A pdb=" N ASN B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 320 removed outlier: 4.063A pdb=" N LEU B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 69 removed outlier: 4.291A pdb=" N LEU C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.925A pdb=" N GLN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.554A pdb=" N LEU C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 113 Processing helix chain 'C' and resid 115 through 122 removed outlier: 3.550A pdb=" N ASP C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 195 removed outlier: 3.634A pdb=" N ILE C 195 " --> pdb=" O GLU C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 192 through 195' Processing helix chain 'C' and resid 207 through 225 removed outlier: 3.637A pdb=" N LEU C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ALA C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 4.310A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.548A pdb=" N ASN C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 320 removed outlier: 4.062A pdb=" N LEU C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 69 removed outlier: 4.290A pdb=" N LEU D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 78 removed outlier: 3.925A pdb=" N GLN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.552A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.549A pdb=" N ASP D 119 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 195 removed outlier: 3.635A pdb=" N ILE D 195 " --> pdb=" O GLU D 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 192 through 195' Processing helix chain 'D' and resid 207 through 225 removed outlier: 3.638A pdb=" N LEU D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 removed outlier: 4.310A pdb=" N LEU D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 285 removed outlier: 3.547A pdb=" N ASN D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 removed outlier: 4.064A pdb=" N LEU D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 69 removed outlier: 4.399A pdb=" N LEU A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.743A pdb=" N GLN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.568A pdb=" N ILE A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.678A pdb=" N ASP A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 225 removed outlier: 3.821A pdb=" N LEU A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LYS A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 4.076A pdb=" N LEU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.770A pdb=" N THR A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 320 removed outlier: 4.055A pdb=" N LEU A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 42 Processing helix chain 'H' and resid 129 through 138 Processing helix chain 'H' and resid 194 through 198 removed outlier: 3.743A pdb=" N ILE H 198 " --> pdb=" O ASN H 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 69 removed outlier: 4.160A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 removed outlier: 3.821A pdb=" N GLN E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 103 through 115 Processing helix chain 'E' and resid 115 through 121 removed outlier: 3.501A pdb=" N ASP E 119 " --> pdb=" O ASP E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 232 removed outlier: 3.558A pdb=" N LEU E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LYS E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER E 228 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 284 removed outlier: 3.525A pdb=" N THR E 273 " --> pdb=" O TYR E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 320 removed outlier: 3.771A pdb=" N LEU E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 69 removed outlier: 4.160A pdb=" N LEU F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 78 removed outlier: 3.821A pdb=" N GLN F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 94 Processing helix chain 'F' and resid 103 through 115 Processing helix chain 'F' and resid 115 through 121 removed outlier: 3.502A pdb=" N ASP F 119 " --> pdb=" O ASP F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 232 removed outlier: 3.558A pdb=" N LEU F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ALA F 216 " --> pdb=" O GLU F 212 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LYS F 217 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER F 228 " --> pdb=" O LYS F 224 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 removed outlier: 3.525A pdb=" N THR F 273 " --> pdb=" O TYR F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 320 removed outlier: 3.770A pdb=" N LEU F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 69 removed outlier: 4.160A pdb=" N LEU G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 78 removed outlier: 3.822A pdb=" N GLN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 94 Processing helix chain 'G' and resid 103 through 115 Processing helix chain 'G' and resid 115 through 121 removed outlier: 3.502A pdb=" N ASP G 119 " --> pdb=" O ASP G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 232 removed outlier: 3.560A pdb=" N LEU G 211 " --> pdb=" O GLY G 207 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ALA G 216 " --> pdb=" O GLU G 212 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LYS G 217 " --> pdb=" O ARG G 213 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU G 226 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER G 228 " --> pdb=" O LYS G 224 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 284 removed outlier: 3.526A pdb=" N THR G 273 " --> pdb=" O TYR G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 320 removed outlier: 3.771A pdb=" N LEU G 314 " --> pdb=" O THR G 310 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 63 through 68 Processing sheet with id=AA2, first strand: chain 'I' and resid 63 through 68 Processing sheet with id=AA3, first strand: chain 'K' and resid 63 through 68 Processing sheet with id=AA4, first strand: chain 'L' and resid 63 through 68 Processing sheet with id=AA5, first strand: chain 'M' and resid 63 through 68 Processing sheet with id=AA6, first strand: chain 'N' and resid 63 through 68 removed outlier: 3.729A pdb=" N ALA N 92 " --> pdb=" O SER N 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2 through 13 current: chain 'B' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 174 through 190 current: chain 'B' and resid 289 through 295 removed outlier: 4.361A pdb=" N THR B 306 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 36 Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 125 Processing sheet with id=AB1, first strand: chain 'C' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 2 through 13 current: chain 'C' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 174 through 190 current: chain 'C' and resid 289 through 295 removed outlier: 4.362A pdb=" N THR C 306 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 36 Processing sheet with id=AB3, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AB4, first strand: chain 'D' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 2 through 13 current: chain 'D' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 174 through 190 current: chain 'D' and resid 289 through 295 removed outlier: 4.362A pdb=" N THR D 306 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 29 through 36 Processing sheet with id=AB6, first strand: chain 'D' and resid 123 through 125 Processing sheet with id=AB7, first strand: chain 'A' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2 through 13 current: chain 'A' and resid 174 through 182 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 174 through 182 current: chain 'A' and resid 289 through 295 removed outlier: 3.698A pdb=" N THR A 306 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 29 through 35 Processing sheet with id=AB9, first strand: chain 'A' and resid 124 through 125 removed outlier: 3.572A pdb=" N VAL A 131 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 68 through 73 removed outlier: 3.838A pdb=" N ASN H 154 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS H 9 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL H 152 " --> pdb=" O LYS H 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 13 through 14 removed outlier: 3.646A pdb=" N PHE H 14 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 161 through 163 removed outlier: 3.737A pdb=" N LYS H 161 " --> pdb=" O GLU H 231 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER H 240 " --> pdb=" O GLU H 228 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR H 230 " --> pdb=" O VAL H 238 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL H 238 " --> pdb=" O TYR H 230 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 167 through 169 Processing sheet with id=AC5, first strand: chain 'H' and resid 173 through 174 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 173 through 174 current: chain 'H' and resid 205 through 213 removed outlier: 3.506A pdb=" N THR H 213 " --> pdb=" O ALA H 218 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA H 218 " --> pdb=" O THR H 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 2 through 13 current: chain 'E' and resid 24 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 24 through 27 current: chain 'E' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 174 through 190 current: chain 'E' and resid 289 through 295 removed outlier: 4.194A pdb=" N THR E 306 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 36 Processing sheet with id=AC8, first strand: chain 'E' and resid 123 through 125 Processing sheet with id=AC9, first strand: chain 'F' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 2 through 13 current: chain 'F' and resid 24 through 27 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 24 through 27 current: chain 'F' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 174 through 190 current: chain 'F' and resid 289 through 295 removed outlier: 4.195A pdb=" N THR F 306 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 29 through 36 Processing sheet with id=AD2, first strand: chain 'F' and resid 123 through 125 Processing sheet with id=AD3, first strand: chain 'G' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 2 through 13 current: chain 'G' and resid 180 through 190 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 180 through 190 current: chain 'G' and resid 289 through 295 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'G' and resid 17 through 18 removed outlier: 4.294A pdb=" N LYS G 26 " --> pdb=" O VAL G 18 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 29 through 36 Processing sheet with id=AD6, first strand: chain 'G' and resid 123 through 125 1071 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 7191 1.04 - 1.23: 1584 1.23 - 1.43: 9072 1.43 - 1.63: 14952 1.63 - 1.83: 156 Bond restraints: 32955 Sorted by residual: bond pdb=" C1' A S 40 " pdb=" N9 A S 40 " ideal model delta sigma weight residual 1.465 1.386 0.079 1.50e-02 4.44e+03 2.79e+01 bond pdb=" C1' A S 43 " pdb=" N9 A S 43 " ideal model delta sigma weight residual 1.465 1.386 0.079 1.50e-02 4.44e+03 2.74e+01 bond pdb=" C1' U S 41 " pdb=" N1 U S 41 " ideal model delta sigma weight residual 1.480 1.552 -0.072 1.50e-02 4.44e+03 2.27e+01 bond pdb=" N LEU F 24 " pdb=" CA LEU F 24 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.22e-02 6.72e+03 1.43e+01 bond pdb=" N ILE E 21 " pdb=" CA ILE E 21 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.40e+01 ... (remaining 32950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.55: 51339 11.55 - 23.09: 4 23.09 - 34.64: 15 34.64 - 46.18: 13 46.18 - 57.73: 8 Bond angle restraints: 51379 Sorted by residual: angle pdb=" C GLN E 78 " pdb=" N TYR E 79 " pdb=" H TYR E 79 " ideal model delta sigma weight residual 124.38 66.65 57.73 3.00e+00 1.11e-01 3.70e+02 angle pdb=" CA TYR E 79 " pdb=" N TYR E 79 " pdb=" H TYR E 79 " ideal model delta sigma weight residual 114.08 56.82 57.26 3.00e+00 1.11e-01 3.64e+02 angle pdb=" C VAL G 18 " pdb=" N GLU G 19 " pdb=" H GLU G 19 " ideal model delta sigma weight residual 124.30 67.41 56.89 3.00e+00 1.11e-01 3.60e+02 angle pdb=" CA GLU G 19 " pdb=" N GLU G 19 " pdb=" H GLU G 19 " ideal model delta sigma weight residual 114.00 58.07 55.93 3.00e+00 1.11e-01 3.48e+02 angle pdb=" C ASN G 11 " pdb=" N LEU G 12 " pdb=" H LEU G 12 " ideal model delta sigma weight residual 123.68 69.75 53.94 3.00e+00 1.11e-01 3.23e+02 ... (remaining 51374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.23: 17585 34.23 - 68.46: 429 68.46 - 102.69: 31 102.69 - 136.92: 1 136.92 - 171.15: 1 Dihedral angle restraints: 18047 sinusoidal: 8648 harmonic: 9399 Sorted by residual: dihedral pdb=" O4' U S 38 " pdb=" C1' U S 38 " pdb=" N1 U S 38 " pdb=" C2 U S 38 " ideal model delta sinusoidal sigma weight residual 232.00 60.85 171.15 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" O4' U S 32 " pdb=" C1' U S 32 " pdb=" N1 U S 32 " pdb=" C2 U S 32 " ideal model delta sinusoidal sigma weight residual 232.00 116.52 115.48 1 1.70e+01 3.46e-03 4.75e+01 dihedral pdb=" O4' U S 2 " pdb=" C1' U S 2 " pdb=" N1 U S 2 " pdb=" C2 U S 2 " ideal model delta sinusoidal sigma weight residual -128.00 -51.12 -76.88 1 1.70e+01 3.46e-03 2.57e+01 ... (remaining 18044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3495 0.076 - 0.152: 533 0.152 - 0.229: 32 0.229 - 0.305: 9 0.305 - 0.381: 3 Chirality restraints: 4072 Sorted by residual: chirality pdb=" CB VAL F 18 " pdb=" CA VAL F 18 " pdb=" CG1 VAL F 18 " pdb=" CG2 VAL F 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CB VAL G 18 " pdb=" CA VAL G 18 " pdb=" CG1 VAL G 18 " pdb=" CG2 VAL G 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB VAL E 18 " pdb=" CA VAL E 18 " pdb=" CG1 VAL E 18 " pdb=" CG2 VAL E 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 4069 not shown) Planarity restraints: 5137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 23 " -0.203 2.00e-02 2.50e+03 4.10e-01 2.52e+03 pdb=" CG ASN E 23 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN E 23 " 0.196 2.00e-02 2.50e+03 pdb=" ND2 ASN E 23 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN E 23 " -0.692 2.00e-02 2.50e+03 pdb="HD22 ASN E 23 " 0.669 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 23 " 0.222 2.00e-02 2.50e+03 3.94e-01 2.33e+03 pdb=" CG ASN F 23 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN F 23 " -0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN F 23 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN F 23 " 0.651 2.00e-02 2.50e+03 pdb="HD22 ASN F 23 " -0.639 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 48 " -0.109 2.00e-02 2.50e+03 5.70e-02 6.50e+01 pdb=" CG TYR N 48 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR N 48 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR N 48 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR N 48 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR N 48 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR N 48 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR N 48 " -0.081 2.00e-02 2.50e+03 ... (remaining 5134 not shown) Histogram of nonbonded interaction distances: 0.92 - 1.66: 20 1.66 - 2.39: 5897 2.39 - 3.13: 54915 3.13 - 3.86: 89309 3.86 - 4.60: 142181 Warning: very small nonbonded interaction distances. Nonbonded interactions: 292322 Sorted by model distance: nonbonded pdb=" O4 U S 38 " pdb=" O1 TRS S 401 " model vdw 0.924 2.800 nonbonded pdb=" HE2 HIS E 55 " pdb=" C2 TRS E 401 " model vdw 1.453 2.200 nonbonded pdb=" H TYR E 79 " pdb=" HA TYR E 79 " model vdw 1.462 1.816 nonbonded pdb=" HB THR G 134 " pdb=" HG1 THR G 134 " model vdw 1.494 1.816 nonbonded pdb=" H VAL E 33 " pdb=" HA VAL E 33 " model vdw 1.538 1.816 ... (remaining 292317 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 19 or resid 25 through 152 or resid 178 through \ 234 or resid 243 through 297 or resid 308 through 320)) selection = (chain 'B' and (resid 1 through 19 or resid 25 through 152 or resid 178 through \ 234 or resid 243 through 297 or resid 308 through 320)) selection = (chain 'C' and (resid 1 through 19 or resid 25 through 152 or resid 178 through \ 234 or resid 243 through 297 or resid 308 through 320)) selection = (chain 'D' and (resid 1 through 19 or resid 25 through 152 or resid 178 through \ 234 or resid 243 through 297 or resid 308 through 320)) selection = (chain 'E' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name SD or name CE )) or (resid 2 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 3 and (name \ N or name CA or name C or name O or name CB or name OG )) or (resid 4 and (name \ N or name CA or name C or name O )) or (resid 5 and (name N or name CA or name \ C or name O or name CB or name OG )) or (resid 6 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2)) or (resid 7 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name NE or name CZ o \ r name NH1 or name NH2)) or (resid 8 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ )) or (resid 9 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2)) or (resid 10 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or (resid 11 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 12 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or nam \ e CD2)) or (resid 13 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name OE1 or name OE2)) or (resid 14 and (name N or name CA o \ r name C or name O or name CB or name OG )) or (resid 15 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 16 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2)) or (resid 17 and (name N or name CA or name C or name O )) or (resid \ 18 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2)) or (resid 19 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name OE1 or name OE2)) or (resid 25 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2)) or (resid 26 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ )) or (resid 27 and (name N or name CA or name C or name O or name CB or name \ CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 28 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD or name NE or nam \ e CZ or name NH1 or name NH2)) or (resid 29 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2)) or (resid 30 and (name N or name CA \ or name C or name O or name CB )) or (resid 31 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or (resid 32 through 33 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (resid \ 34 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2)) or (resid 35 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ )) or (resid 36 and (name N or name \ CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 37 and (n \ ame N or name CA or name C or name O or name CB or name OG )) or (resid 38 and ( \ name N or name CA or name C or name O or name CB or name OG1 or name CG2)) or (r \ esid 39 and (name N or name CA or name C or name O )) or (resid 40 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or n \ ame CE1 or name CE2 or name CZ or name OH )) or (resid 41 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 4 \ 2 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2) \ ) or (resid 43 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 44 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ or name CE1 or name CE2 or name CZ or name OH )) or (resid 45 and (name N or na \ me CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 46 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or (r \ esid 47 and (name N or name CA or name C or name O or name CB or name CG1 or nam \ e CG2)) or (resid 48 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1)) or (resid 49 and (name N or name CA or name C o \ r name O or name CB or name OG )) or (resid 50 and (name N or name CA or name C \ or name O )) or (resid 51 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2)) or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or (resid 53 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 54 and ( \ name N or name CA or name C or name O or name CB )) or (resid 55 and (name N or \ name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or nam \ e CE1 or name NE2)) or (resid 56 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 57 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) \ or (resid 58 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name OE1 or name NE2)) or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or (resid 60 and (name N or name CA or name C or name \ O or name CB or name OG )) or (resid 61 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2)) or (resid 62 and (name N or n \ ame CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 63 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or nam \ e OD2)) or (resid 64 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1)) or (resid 65 and (name N or name CA or name C o \ r name O or name CB )) or (resid 66 through 67 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ )) or (resid 68 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name OE2)) or (resid 69 and (name N or name CA or name C or name O ) \ ) or (resid 70 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2)) or (resid 71 and (name N or name CA or name C or name \ O or name CB or name CG or name CD )) or (resid 72 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2)) or (resid 73 and (name N or n \ ame CA or name C or name O )) or (resid 74 and (name N or name CA or name C or n \ ame O or name CB or name OG )) or (resid 75 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2)) or (resid 76 through 77 a \ nd (name N or name CA or name C or name O or name CB or name OG )) or (resid 78 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame OE1 or name NE2)) or (resid 79 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ o \ r name OH )) or (resid 80 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2)) or (resid 81 and (name N or name \ CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE \ 1 or name CE2 or name CZ )) or (resid 82 and (name N or name CA or name C or nam \ e O or name CB or name CG1 or name CG2 or name CD1)) or (resid 83 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ )) or (resid 84 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 85 \ and (name N or name CA or name C or name O or name CB or name OG )) or (resid 86 \ and (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) \ or (resid 87 and (name N or name CA or name C or name O or name CB or name CG o \ r name OD1 or name OD2)) or (resid 88 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name OE1 or name OE2)) or (resid 89 and (na \ me N or name CA or name C or name O or name CB )) or (resid 90 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (re \ sid 91 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ )) or (resid 92 and (name N or name CA or name C or nam \ e O or name CB or name CG1 or name CG2 or name CD1)) or (resid 93 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e OE2)) or (resid 94 and (name N or name CA or name C or name O )) or (resid 95 \ and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or \ name CD1)) or (resid 96 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ )) or (resid 97 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) \ or (resid 98 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD )) or (resid 99 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ )) or (resid 100 and (name N or name \ CA or name C or name O or name CB or name CG or name OD1 or name OD2)) or (resi \ d 101 and (name N or name CA or name C or name O or name CB or name CG or name C \ D1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 102 an \ d (name N or name CA or name C or name O or name CB or name CG or name OD1 or na \ me ND2)) or (resid 103 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2)) or (resid 104 and (name N or name CA or name C \ or name O or name CB )) or (resid 105 through 106 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 107 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or ( \ resid 108 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1 or name OE2)) or (resid 109 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2)) or (resid 110 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name OE2) \ ) or (resid 111 and (name N or name CA or name C or name O or name CB or name CG \ 1 or name CG2)) or (resid 112 and (name N or name CA or name C or name O or name \ CB or name CG or name SD or name CE )) or (resid 113 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 114 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me CE or name NZ )) or (resid 115 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name OD2)) or (resid 116 and (name N or name C \ A or name C or name O or name CB or name CG1 or name CG2)) or (resid 117 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2 or name C \ D1)) or (resid 118 and (name N or name CA or name C or name O or name CB )) or ( \ resid 119 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name OD2)) or (resid 120 and (name N or name CA or name C or name O or \ name CB or name CG1 or name CG2)) or (resid 121 through 122 and (name N or name \ CA or name C or name O )) or (resid 123 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ )) or (resid 124 and (name N or name CA or name C or name O or name CB or n \ ame CG or name SD or name CE )) or (resid 125 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 o \ r name CZ or name OH )) or (resid 126 and (name N or name CA or name C or name O \ or name CB )) or (resid 127 through 128 and (name N or name CA or name C or nam \ e O )) or (resid 129 and (name N or name CA or name C or name O or name CB )) or \ (resid 130 and (name N or name CA or name C or name O or name CB or name CG or \ name CD )) or (resid 131 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2)) or (resid 132 through 133 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 134 and (name N or name CA or name C or name O or name \ CB or name OG1 or name CG2)) or (resid 135 and (name N or name CA or name C or n \ ame O or name CB or name OG )) or (resid 136 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or na \ me NH2)) or (resid 137 and (name N or name CA or name C or name O or name CB or \ name CG1 or name CG2 or name CD1)) or (resid 138 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )) or (resid \ 139 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2)) or (resid 140 and (name N or name CA or name C or name O )) or (r \ esid 141 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 142 \ and (name N or name CA or name C or name O or name CB or name CG or name SD or \ name CE )) or (resid 143 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1)) or (resid 144 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or (resid 145 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 146 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 147 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame NE or name CZ or name NH1 or name NH2)) or (resid 148 and (name N or name CA \ or name C or name O )) or (resid 149 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2)) or (resid 150 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name OE1 or name O \ E2)) or (resid 151 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1)) or (resid 152 and (name N or name CA or name C or \ name O or name CB or name CG or name CD )) or (resid 178 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) \ or (resid 179 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2)) or (resid 180 through 181 and (name N or name CA or name C or name \ O or name CB or name OG )) or (resid 182 and (name N or name CA or name C or na \ me O or name CB )) or (resid 183 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD1 or name CD2)) or (resid 184 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 o \ r name CE2 or name CZ or name OH )) or (resid 185 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2)) or (resid 186 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ )) or (resid 187 and (name N or name CA or name C or \ name O or name CB or name OG )) or (resid 188 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or (resid 189 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name OE1 or name OE2)) or (resid 190 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (r \ esid 191 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name OD2)) or (resid 192 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name OE2)) or (resid 193 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or (resid 194 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2)) or (resid 195 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1)) or (resid 196 and (name N or \ name CA or name C or name O or name CB )) or (resid 197 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2)) or (resid 198 and (name \ N or name CA or name C or name O or name CB or name CG or name CD )) or (resid \ 199 and (name N or name CA or name C or name O or name CB or name OG )) or (resi \ d 200 and (name N or name CA or name C or name O or name CB or name OG1 or name \ CG2)) or (resid 201 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 202 \ and (name N or name CA or name C or name O )) or (resid 203 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name OE2 \ )) or (resid 204 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name CE or name NZ )) or (resid 205 and (name N or name CA or na \ me C or name O or name CB or name CG1 or name CG2)) or (resid 206 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ )) or (resid 207 and (name N or name CA or name C or name O )) or (resid 208 \ through 210 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name OE1 or name OE2)) or (resid 211 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 212 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name OE \ 1 or name OE2)) or (resid 213 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (re \ sid 214 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name NE2)) or (resid 215 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE or name NZ )) or (resid 216 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 217 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE or \ name NZ )) or (resid 218 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 2 \ 19 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 \ )) or (resid 220 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name CE or name NZ )) or (resid 221 and (name N or name CA or na \ me C or name O or name CB or name OG )) or (resid 222 and (name N or name CA or \ name C or name O or name CB )) or (resid 223 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 224 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE or \ name NZ )) or (resid 225 and (name N or name CA or name C or name O or name CB \ )) or (resid 226 and (name N or name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or (resid 227 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or na \ me CZ or name OH )) or (resid 228 and (name N or name CA or name C or name O or \ name CB or name OG )) or (resid 229 through 230 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2)) or (resid 231 and (na \ me N or name CA or name C or name O or name CB or name OG )) or (resid 232 and ( \ name N or name CA or name C or name O )) or (resid 233 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 234 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2 or name CE1 or name CE2 or name CZ )) or (resid 243 and (name N or name \ CA or name C or name O or name CB or name CG or name CD )) or (resid 244 and (n \ ame N or name CA or name C or name O or name CB or name OG )) or (resid 245 and \ (name N or name CA or name C or name O or name CB or name CG or name SD or name \ CE )) or (resid 246 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name CE or name NZ )) or (resid 247 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 248 \ and (name N or name CA or name C or name O or name CB or name CG or name SD or n \ ame CE )) or (resid 249 and (name N or name CA or name C or name O or name CB or \ name OG )) or (resid 250 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2)) or (resid 251 through 252 and (name N or na \ me CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 253 and \ (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) or \ (resid 254 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ )) or (resid 255 and (name N or name CA or name C o \ r name O or name CB or name OG1 or name CG2)) or (resid 256 and (name N or name \ CA or name C or name O or name CB or name CG or name OD1 or name OD2)) or (resid \ 257 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 258 and (name N or \ name CA or name C or name O or name CB or name CG or name CD )) or (resid 259 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD1 or n \ ame CD2 or name CE1 or name CE2 or name CZ )) or (resid 260 and (name N or name \ CA or name C or name O or name CB or name CG or name SD or name CE )) or (resid \ 261 and (name N or name CA or name C or name O or name CB or name CG or name CD \ )) or (resid 262 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name OE1 or name OE2)) or (resid 263 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD )) or (resid 264 and (name N or \ name CA or name C or name O or name CB )) or (resid 265 and (name N or name CA \ or name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or \ name NE2)) or (resid 266 through 268 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2)) or (resid 269 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ or name OH )) or (resid 270 and (name N or name CA or \ name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 271 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name CE or name NZ )) or (resid 272 through 273 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2)) or (resid 274 and (name N or nam \ e CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (re \ sid 275 and (name N or name CA or name C or name O or name CB or name CG or name \ SD or name CE )) or (resid 276 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or ( \ resid 277 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD1 or name CD2)) or (resid 278 and (name N or name CA or name C or name O )) \ or (resid 279 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ )) or (resid 280 and (name N or name CA or name \ C or name O or name CB )) or (resid 281 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ )) or (resid 282 and \ (name N or name CA or name C or name O )) or (resid 283 and (name N or name CA o \ r name C or name O or name CB or name CG1 or name CG2)) or (resid 284 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2)) \ or (resid 285 and (name N or name CA or name C or name O or name CB or name CG \ or name OD1 or name ND2)) or (resid 286 and (name N or name CA or name C or name \ O )) or (resid 287 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name ND2)) or (resid 288 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2)) or (resid 289 and (name \ N or name CA or name C or name O or name CB )) or (resid 290 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name CE or name NZ ) \ ) or (resid 291 and (name N or name CA or name C or name O or name CB )) or (res \ id 292 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 293 a \ nd (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) o \ r (resid 294 and (name N or name CA or name C or name O or name CB or name CG1 o \ r name CG2 or name CD1)) or (resid 295 through 296 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 297 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ OE1 or name OE2)) or (resid 308 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD1 or name CD2)) or (resid 309 and (name N or name CA \ or name C or name O or name CB or name OG )) or (resid 310 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2)) or (resid 311 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (res \ id 312 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2)) or (resid 313 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name OD2)) or (resid 314 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2)) o \ r (resid 315 through 316 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2)) or (resid 317 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name CE or name NZ )) or (resid 318 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)) or (resid 319 through 320 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name OE1 or name OE2)))) selection = (chain 'F' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name SD or name CE )) or (resid 2 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 3 and (name \ N or name CA or name C or name O or name CB or name OG )) or (resid 4 and (name \ N or name CA or name C or name O )) or (resid 5 and (name N or name CA or name \ C or name O or name CB or name OG )) or (resid 6 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2)) or (resid 7 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name NE or name CZ o \ r name NH1 or name NH2)) or (resid 8 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ )) or (resid 9 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2)) or (resid 10 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or (resid 11 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 12 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or nam \ e CD2)) or (resid 13 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name OE1 or name OE2)) or (resid 14 and (name N or name CA o \ r name C or name O or name CB or name OG )) or (resid 15 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 16 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2)) or (resid 17 and (name N or name CA or name C or name O )) or (resid \ 18 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2)) or (resid 19 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name OE1 or name OE2)) or (resid 25 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2)) or (resid 26 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ )) or (resid 27 and (name N or name CA or name C or name O or name CB or name \ CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 28 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD or name NE or nam \ e CZ or name NH1 or name NH2)) or (resid 29 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2)) or (resid 30 and (name N or name CA \ or name C or name O or name CB )) or (resid 31 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or (resid 32 through 33 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (resid \ 34 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2)) or (resid 35 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ )) or (resid 36 and (name N or name \ CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 37 and (n \ ame N or name CA or name C or name O or name CB or name OG )) or (resid 38 and ( \ name N or name CA or name C or name O or name CB or name OG1 or name CG2)) or (r \ esid 39 and (name N or name CA or name C or name O )) or (resid 40 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or n \ ame CE1 or name CE2 or name CZ or name OH )) or (resid 41 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 4 \ 2 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2) \ ) or (resid 43 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 44 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ or name CE1 or name CE2 or name CZ or name OH )) or (resid 45 and (name N or na \ me CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 46 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or (r \ esid 47 and (name N or name CA or name C or name O or name CB or name CG1 or nam \ e CG2)) or (resid 48 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1)) or (resid 49 and (name N or name CA or name C o \ r name O or name CB or name OG )) or (resid 50 and (name N or name CA or name C \ or name O )) or (resid 51 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2)) or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or (resid 53 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 54 and ( \ name N or name CA or name C or name O or name CB )) or (resid 55 and (name N or \ name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or nam \ e CE1 or name NE2)) or (resid 56 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 57 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) \ or (resid 58 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name OE1 or name NE2)) or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or (resid 60 and (name N or name CA or name C or name \ O or name CB or name OG )) or (resid 61 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2)) or (resid 62 and (name N or n \ ame CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 63 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or nam \ e OD2)) or (resid 64 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1)) or (resid 65 and (name N or name CA or name C o \ r name O or name CB )) or (resid 66 through 67 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ )) or (resid 68 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name OE2)) or (resid 69 and (name N or name CA or name C or name O ) \ ) or (resid 70 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2)) or (resid 71 and (name N or name CA or name C or name \ O or name CB or name CG or name CD )) or (resid 72 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2)) or (resid 73 and (name N or n \ ame CA or name C or name O )) or (resid 74 and (name N or name CA or name C or n \ ame O or name CB or name OG )) or (resid 75 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2)) or (resid 76 through 77 a \ nd (name N or name CA or name C or name O or name CB or name OG )) or (resid 78 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame OE1 or name NE2)) or (resid 79 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ o \ r name OH )) or (resid 80 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2)) or (resid 81 and (name N or name \ CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE \ 1 or name CE2 or name CZ )) or (resid 82 and (name N or name CA or name C or nam \ e O or name CB or name CG1 or name CG2 or name CD1)) or (resid 83 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ )) or (resid 84 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 85 \ and (name N or name CA or name C or name O or name CB or name OG )) or (resid 86 \ and (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) \ or (resid 87 and (name N or name CA or name C or name O or name CB or name CG o \ r name OD1 or name OD2)) or (resid 88 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name OE1 or name OE2)) or (resid 89 and (na \ me N or name CA or name C or name O or name CB )) or (resid 90 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (re \ sid 91 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ )) or (resid 92 and (name N or name CA or name C or nam \ e O or name CB or name CG1 or name CG2 or name CD1)) or (resid 93 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e OE2)) or (resid 94 and (name N or name CA or name C or name O )) or (resid 95 \ and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or \ name CD1)) or (resid 96 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ )) or (resid 97 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) \ or (resid 98 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD )) or (resid 99 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ )) or (resid 100 and (name N or name \ CA or name C or name O or name CB or name CG or name OD1 or name OD2)) or (resi \ d 101 and (name N or name CA or name C or name O or name CB or name CG or name C \ D1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 102 an \ d (name N or name CA or name C or name O or name CB or name CG or name OD1 or na \ me ND2)) or (resid 103 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2)) or (resid 104 and (name N or name CA or name C \ or name O or name CB )) or (resid 105 through 106 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 107 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or ( \ resid 108 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1 or name OE2)) or (resid 109 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2)) or (resid 110 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name OE2) \ ) or (resid 111 and (name N or name CA or name C or name O or name CB or name CG \ 1 or name CG2)) or (resid 112 and (name N or name CA or name C or name O or name \ CB or name CG or name SD or name CE )) or (resid 113 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 114 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me CE or name NZ )) or (resid 115 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name OD2)) or (resid 116 and (name N or name C \ A or name C or name O or name CB or name CG1 or name CG2)) or (resid 117 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2 or name C \ D1)) or (resid 118 and (name N or name CA or name C or name O or name CB )) or ( \ resid 119 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name OD2)) or (resid 120 and (name N or name CA or name C or name O or \ name CB or name CG1 or name CG2)) or (resid 121 through 122 and (name N or name \ CA or name C or name O )) or (resid 123 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ )) or (resid 124 and (name N or name CA or name C or name O or name CB or n \ ame CG or name SD or name CE )) or (resid 125 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 o \ r name CZ or name OH )) or (resid 126 and (name N or name CA or name C or name O \ or name CB )) or (resid 127 through 128 and (name N or name CA or name C or nam \ e O )) or (resid 129 and (name N or name CA or name C or name O or name CB )) or \ (resid 130 and (name N or name CA or name C or name O or name CB or name CG or \ name CD )) or (resid 131 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2)) or (resid 132 through 133 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 134 and (name N or name CA or name C or name O or name \ CB or name OG1 or name CG2)) or (resid 135 and (name N or name CA or name C or n \ ame O or name CB or name OG )) or (resid 136 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or na \ me NH2)) or (resid 137 and (name N or name CA or name C or name O or name CB or \ name CG1 or name CG2 or name CD1)) or (resid 138 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )) or (resid \ 139 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2)) or (resid 140 and (name N or name CA or name C or name O )) or (r \ esid 141 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 142 \ and (name N or name CA or name C or name O or name CB or name CG or name SD or \ name CE )) or (resid 143 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1)) or (resid 144 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or (resid 145 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 146 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 147 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame NE or name CZ or name NH1 or name NH2)) or (resid 148 and (name N or name CA \ or name C or name O )) or (resid 149 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2)) or (resid 150 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name OE1 or name O \ E2)) or (resid 151 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1)) or (resid 152 and (name N or name CA or name C or \ name O or name CB or name CG or name CD )) or (resid 178 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) \ or (resid 179 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2)) or (resid 180 through 181 and (name N or name CA or name C or name \ O or name CB or name OG )) or (resid 182 and (name N or name CA or name C or na \ me O or name CB )) or (resid 183 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD1 or name CD2)) or (resid 184 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 o \ r name CE2 or name CZ or name OH )) or (resid 185 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2)) or (resid 186 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ )) or (resid 187 and (name N or name CA or name C or \ name O or name CB or name OG )) or (resid 188 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or (resid 189 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name OE1 or name OE2)) or (resid 190 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (r \ esid 191 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name OD2)) or (resid 192 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name OE2)) or (resid 193 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or (resid 194 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2)) or (resid 195 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1)) or (resid 196 and (name N or \ name CA or name C or name O or name CB )) or (resid 197 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2)) or (resid 198 and (name \ N or name CA or name C or name O or name CB or name CG or name CD )) or (resid \ 199 and (name N or name CA or name C or name O or name CB or name OG )) or (resi \ d 200 and (name N or name CA or name C or name O or name CB or name OG1 or name \ CG2)) or (resid 201 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 202 \ and (name N or name CA or name C or name O )) or (resid 203 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name OE2 \ )) or (resid 204 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name CE or name NZ )) or (resid 205 and (name N or name CA or na \ me C or name O or name CB or name CG1 or name CG2)) or (resid 206 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ )) or (resid 207 and (name N or name CA or name C or name O )) or (resid 208 \ through 210 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name OE1 or name OE2)) or (resid 211 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 212 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name OE \ 1 or name OE2)) or (resid 213 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (re \ sid 214 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name NE2)) or (resid 215 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE or name NZ )) or (resid 216 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 217 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE or \ name NZ )) or (resid 218 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 2 \ 19 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 \ )) or (resid 220 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name CE or name NZ )) or (resid 221 and (name N or name CA or na \ me C or name O or name CB or name OG )) or (resid 222 and (name N or name CA or \ name C or name O or name CB )) or (resid 223 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 224 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE or \ name NZ )) or (resid 225 and (name N or name CA or name C or name O or name CB \ )) or (resid 226 and (name N or name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or (resid 227 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or na \ me CZ or name OH )) or (resid 228 and (name N or name CA or name C or name O or \ name CB or name OG )) or (resid 229 through 230 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2)) or (resid 231 and (na \ me N or name CA or name C or name O or name CB or name OG )) or (resid 232 and ( \ name N or name CA or name C or name O )) or (resid 233 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 234 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2 or name CE1 or name CE2 or name CZ )) or (resid 243 and (name N or name \ CA or name C or name O or name CB or name CG or name CD )) or (resid 244 and (n \ ame N or name CA or name C or name O or name CB or name OG )) or (resid 245 and \ (name N or name CA or name C or name O or name CB or name CG or name SD or name \ CE )) or (resid 246 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name CE or name NZ )) or (resid 247 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 248 \ and (name N or name CA or name C or name O or name CB or name CG or name SD or n \ ame CE )) or (resid 249 and (name N or name CA or name C or name O or name CB or \ name OG )) or (resid 250 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2)) or (resid 251 through 252 and (name N or na \ me CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 253 and \ (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) or \ (resid 254 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ )) or (resid 255 and (name N or name CA or name C o \ r name O or name CB or name OG1 or name CG2)) or (resid 256 and (name N or name \ CA or name C or name O or name CB or name CG or name OD1 or name OD2)) or (resid \ 257 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 258 and (name N or \ name CA or name C or name O or name CB or name CG or name CD )) or (resid 259 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD1 or n \ ame CD2 or name CE1 or name CE2 or name CZ )) or (resid 260 and (name N or name \ CA or name C or name O or name CB or name CG or name SD or name CE )) or (resid \ 261 and (name N or name CA or name C or name 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N or name CA or name C \ or name O or name CB or name OG1 or name CG2)) or (resid 274 and (name N or nam \ e CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (re \ sid 275 and (name N or name CA or name C or name O or name CB or name CG or name \ SD or name CE )) or (resid 276 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or ( \ resid 277 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD1 or name CD2)) or (resid 278 and (name N or name CA or name C or name O )) \ or (resid 279 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ )) or (resid 280 and (name N or name CA or name \ C or name O or name CB )) or (resid 281 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ )) or (resid 282 and \ (name N or name CA or name C or name O )) or (resid 283 and (name N or name CA o \ r name C or name O or name CB or name CG1 or name CG2)) or (resid 284 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2)) \ or (resid 285 and (name N or name CA or name C or name O or name CB or name CG \ or name OD1 or name ND2)) or (resid 286 and (name N or name CA or name C or name \ O )) or (resid 287 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name ND2)) or (resid 288 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2)) or (resid 289 and (name \ N or name CA or name C or name O or name CB )) or (resid 290 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name CE or name NZ ) \ ) or (resid 291 and (name N or name CA or name C or name O or name CB )) or (res \ id 292 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 293 a \ nd (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) o \ r (resid 294 and (name N or name CA or name C or name O or name CB or name CG1 o \ r name CG2 or name CD1)) or (resid 295 through 296 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 297 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ OE1 or name OE2)) or (resid 308 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD1 or name CD2)) or (resid 309 and (name N or name CA \ or name C or name O or name CB or name OG )) or (resid 310 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2)) or (resid 311 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (res \ id 312 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2)) or (resid 313 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name OD2)) or (resid 314 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2)) o \ r (resid 315 through 316 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2)) or (resid 317 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name CE or name NZ )) or (resid 318 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)) or (resid 319 through 320 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name OE1 or name OE2)))) selection = (chain 'G' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name SD or name CE )) or (resid 2 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 3 and (name \ N or name CA or name C or name O or name CB or name OG )) or (resid 4 and (name \ N or name CA or name C or name O )) or (resid 5 and (name N or name CA or name \ C or name O or name CB or name OG )) or (resid 6 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2)) or (resid 7 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name NE or name CZ o \ r name NH1 or name NH2)) or (resid 8 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ )) or (resid 9 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2)) or (resid 10 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or (resid 11 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 12 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or nam \ e CD2)) or (resid 13 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name OE1 or name OE2)) or (resid 14 and (name N or name CA o \ r name C or name O or name CB or name OG )) or (resid 15 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 16 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2)) or (resid 17 and (name N or name CA or name C or name O )) or (resid \ 18 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2)) or (resid 19 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name OE1 or name OE2)) or (resid 25 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2)) or (resid 26 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ )) or (resid 27 and (name N or name CA or name C or name O or name CB or name \ CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 28 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD or name NE or nam \ e CZ or name NH1 or name NH2)) or (resid 29 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2)) or (resid 30 and (name N or name CA \ or name C or name O or name CB )) or (resid 31 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or (resid 32 through 33 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (resid \ 34 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2)) or (resid 35 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ )) or (resid 36 and (name N or name \ CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 37 and (n \ ame N or name CA or name C or name O or name CB or name OG )) or (resid 38 and ( \ name N or name CA or name C or name O or name CB or name OG1 or name CG2)) or (r \ esid 39 and (name N or name CA or name C or name O )) or (resid 40 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or n \ ame CE1 or name CE2 or name CZ or name OH )) or (resid 41 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 4 \ 2 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2) \ ) or (resid 43 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 44 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ or name CE1 or name CE2 or name CZ or name OH )) or (resid 45 and (name N or na \ me CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 46 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or (r \ esid 47 and (name N or name CA or name C or name O or name CB or name CG1 or nam \ e CG2)) or (resid 48 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1)) or (resid 49 and (name N or name CA or name C o \ r name O or name CB or name OG )) or (resid 50 and (name N or name CA or name C \ or name O )) or (resid 51 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2)) or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or (resid 53 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 54 and ( \ name N or name CA or name C or name O or name CB )) or (resid 55 and (name N or \ name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or nam \ e CE1 or name NE2)) or (resid 56 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 57 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) \ or (resid 58 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name OE1 or name NE2)) or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or (resid 60 and (name N or name CA or name C or name \ O or name CB or name OG )) or (resid 61 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2)) or (resid 62 and (name N or n \ ame CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 63 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or nam \ e OD2)) or (resid 64 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1)) or (resid 65 and (name N or name CA or name C o \ r name O or name CB )) or (resid 66 through 67 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ )) or (resid 68 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name OE2)) or (resid 69 and (name N or name CA or name C or name O ) \ ) or (resid 70 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2)) or (resid 71 and (name N or name CA or name C or name \ O or name CB or name CG or name CD )) or (resid 72 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2)) or (resid 73 and (name N or n \ ame CA or name C or name O )) or (resid 74 and (name N or name CA or name C or n \ ame O or name CB or name OG )) or (resid 75 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2)) or (resid 76 through 77 a \ nd (name N or name CA or name C or name O or name CB or name OG )) or (resid 78 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame OE1 or name NE2)) or (resid 79 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ o \ r name OH )) or (resid 80 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2)) or (resid 81 and (name N or name \ CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE \ 1 or name CE2 or name CZ )) or (resid 82 and (name N or name CA or name C or nam \ e O or name CB or name CG1 or name CG2 or name CD1)) or (resid 83 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ )) or (resid 84 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 85 \ and (name N or name CA or name C or name O or name CB or name OG )) or (resid 86 \ and (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) \ or (resid 87 and (name N or name CA or name C or name O or name CB or name CG o \ r name OD1 or name OD2)) or (resid 88 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name OE1 or name OE2)) or (resid 89 and (na \ me N or name CA or name C or name O or name CB )) or (resid 90 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (re \ sid 91 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ )) or (resid 92 and (name N or name CA or name C or nam \ e O or name CB or name CG1 or name CG2 or name CD1)) or (resid 93 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e OE2)) or (resid 94 and (name N or name CA or name C or name O )) or (resid 95 \ and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or \ name CD1)) or (resid 96 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ )) or (resid 97 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) \ or (resid 98 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD )) or (resid 99 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ )) or (resid 100 and (name N or name \ CA or name C or name O or name CB or name CG or name OD1 or name OD2)) or (resi \ d 101 and (name N or name CA or name C or name O or name CB or name CG or name C \ D1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 102 an \ d (name N or name CA or name C or name O or name CB or name CG or name OD1 or na \ me ND2)) or (resid 103 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2)) or (resid 104 and (name N or name CA or name C \ or name O or name CB )) or (resid 105 through 106 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 107 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or ( \ resid 108 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1 or name OE2)) or (resid 109 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2)) or (resid 110 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name OE2) \ ) or (resid 111 and (name N or name CA or name C or name O or name CB or name CG \ 1 or name CG2)) or (resid 112 and (name N or name CA or name C or name O or name \ CB or name CG or name SD or name CE )) or (resid 113 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 114 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me CE or name NZ )) or (resid 115 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name OD2)) or (resid 116 and (name N or name C \ A or name C or name O or name CB or name CG1 or name CG2)) or (resid 117 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2 or name C \ D1)) or (resid 118 and (name N or name CA or name C or name O or name CB )) or ( \ resid 119 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name OD2)) or (resid 120 and (name N or name CA or name C or name O or \ name CB or name CG1 or name CG2)) or (resid 121 through 122 and (name N or name \ CA or name C or name O )) or (resid 123 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ )) or (resid 124 and (name N or name CA or name C or name O or name CB or n \ ame CG or name SD or name CE )) or (resid 125 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 o \ r name CZ or name OH )) or (resid 126 and (name N or name CA or name C or name O \ or name CB )) or (resid 127 through 128 and (name N or name CA or name C or nam \ e O )) or (resid 129 and (name N or name CA or name C or name O or name CB )) or \ (resid 130 and (name N or name CA or name C or name O or name CB or name CG or \ name CD )) or (resid 131 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2)) or (resid 132 through 133 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 134 and (name N or name CA or name C or name O or name \ CB or name OG1 or name CG2)) or (resid 135 and (name N or name CA or name C or n \ ame O or name CB or name OG )) or (resid 136 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or na \ me NH2)) or (resid 137 and (name N or name CA or name C or name O or name CB or \ name CG1 or name CG2 or name CD1)) or (resid 138 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )) or (resid \ 139 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2)) or (resid 140 and (name N or name CA or name C or name O )) or (r \ esid 141 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 142 \ and (name N or name CA or name C or name O or name CB or name CG or name SD or \ name CE )) or (resid 143 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1)) or (resid 144 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or (resid 145 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 146 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 147 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame NE or name CZ or name NH1 or name NH2)) or (resid 148 and (name N or name CA \ or name C or name O )) or (resid 149 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2)) or (resid 150 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name OE1 or name O \ E2)) or (resid 151 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1)) or (resid 152 and (name N or name CA or name C or \ name O or name CB or name CG or name CD )) or (resid 178 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) \ or (resid 179 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2)) or (resid 180 through 181 and (name N or name CA or name C or name \ O or name CB or name OG )) or (resid 182 and (name N or name CA or name C or na \ me O or name CB )) or (resid 183 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD1 or name CD2)) or (resid 184 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 o \ r name CE2 or name CZ or name OH )) or (resid 185 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2)) or (resid 186 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ )) or (resid 187 and (name N or name CA or name C or \ name O or name CB or name OG )) or (resid 188 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or (resid 189 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name OE1 or name OE2)) or (resid 190 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (r \ esid 191 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name OD2)) or (resid 192 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name OE2)) or (resid 193 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or (resid 194 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2)) or (resid 195 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1)) or (resid 196 and (name N or \ name CA or name C or name O or name CB )) or (resid 197 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2)) or (resid 198 and (name \ N or name CA or name C or name O or name CB or name CG or name CD )) or (resid \ 199 and (name N or name CA or name C or name O or name CB or name OG )) or (resi \ d 200 and (name N or name CA or name C or name O or name CB or name OG1 or name \ CG2)) or (resid 201 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 202 \ and (name N or name CA or name C or name O )) or (resid 203 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name OE2 \ )) or (resid 204 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name CE or name NZ )) or (resid 205 and (name N or name CA or na \ me C or name O or name CB or name CG1 or name CG2)) or (resid 206 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ )) or (resid 207 and (name N or name CA or name C or name O )) or (resid 208 \ through 210 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name OE1 or name OE2)) or (resid 211 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 212 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name OE \ 1 or name OE2)) or (resid 213 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (re \ sid 214 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name NE2)) or (resid 215 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE or name NZ )) or (resid 216 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 217 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE or \ name NZ )) or (resid 218 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 2 \ 19 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 \ )) or (resid 220 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name CE or name NZ )) or (resid 221 and (name N or name CA or na \ me C or name O or name CB or name OG )) or (resid 222 and (name N or name CA or \ name C or name O or name CB )) or (resid 223 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 224 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE or \ name NZ )) or (resid 225 and (name N or name CA or name C or name O or name CB \ )) or (resid 226 and (name N or name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or (resid 227 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or na \ me CZ or name OH )) or (resid 228 and (name N or name CA or name C or name O or \ name CB or name OG )) or (resid 229 through 230 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2)) or (resid 231 and (na \ me N or name CA or name C or name O or name CB or name OG )) or (resid 232 and ( \ name N or name CA or name C or name O )) or (resid 233 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 234 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2 or name CE1 or name CE2 or name CZ )) or (resid 243 and (name N or name \ CA or name C or name O or name CB or name CG or name CD )) or (resid 244 and (n \ ame N or name CA or name C or name O or name CB or name OG )) or (resid 245 and \ (name N or name CA or name C or name O or name CB or name CG or name SD or name \ CE )) or (resid 246 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name CE or name NZ )) or (resid 247 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 248 \ and (name N or name CA or name C or name O or name CB or name CG or name SD or n \ ame CE )) or (resid 249 and (name N or name CA or name C or name O or name CB or \ name OG )) or (resid 250 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2)) or (resid 251 through 252 and (name N or na \ me CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 253 and \ (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) or \ (resid 254 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ )) or (resid 255 and (name N or name CA or name C o \ r name O or name CB or name OG1 or name CG2)) or (resid 256 and (name N or name \ CA or name C or name O or name CB or name CG or name OD1 or name OD2)) or (resid \ 257 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 258 and (name N or \ name CA or name C or name O or name CB or name CG or name CD )) or (resid 259 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD1 or n \ ame CD2 or name CE1 or name CE2 or name CZ )) or (resid 260 and (name N or name \ CA or name C or name O or name CB or name CG or name SD or name CE )) or (resid \ 261 and (name N or name CA or name C or name O or name CB or name CG or name CD \ )) or (resid 262 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name OE1 or name OE2)) or (resid 263 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD )) or (resid 264 and (name N or \ name CA or name C or name O or name CB )) or (resid 265 and (name N or name CA \ or name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or \ name NE2)) or (resid 266 through 268 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2)) or (resid 269 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ or name OH )) or (resid 270 and (name N or name CA or \ name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 271 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name CE or name NZ )) or (resid 272 through 273 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2)) or (resid 274 and (name N or nam \ e CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (re \ sid 275 and (name N or name CA or name C or name O or name CB or name CG or name \ SD or name CE )) or (resid 276 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or ( \ resid 277 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD1 or name CD2)) or (resid 278 and (name N or name CA or name C or name O )) \ or (resid 279 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ )) or (resid 280 and (name N or name CA or name \ C or name O or name CB )) or (resid 281 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ )) or (resid 282 and \ (name N or name CA or name C or name O )) or (resid 283 and (name N or name CA o \ r name C or name O or name CB or name CG1 or name CG2)) or (resid 284 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2)) \ or (resid 285 and (name N or name CA or name C or name O or name CB or name CG \ or name OD1 or name ND2)) or (resid 286 and (name N or name CA or name C or name \ O )) or (resid 287 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name ND2)) or (resid 288 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2)) or (resid 289 and (name \ N or name CA or name C or name O or name CB )) or (resid 290 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name CE or name NZ ) \ ) or (resid 291 and (name N or name CA or name C or name O or name CB )) or (res \ id 292 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 293 a \ nd (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) o \ r (resid 294 and (name N or name CA or name C or name O or name CB or name CG1 o \ r name CG2 or name CD1)) or (resid 295 through 296 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 297 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ OE1 or name OE2)) or (resid 308 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD1 or name CD2)) or (resid 309 and (name N or name CA \ or name C or name O or name CB or name OG )) or (resid 310 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2)) or (resid 311 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (res \ id 312 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2)) or (resid 313 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name OD2)) or (resid 314 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2)) o \ r (resid 315 through 316 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2)) or (resid 317 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name CE or name NZ )) or (resid 318 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)) or (resid 319 through 320 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name OE1 or name OE2)))) } ncs_group { reference = (chain 'I' and resid 6 through 138) selection = (chain 'J' and resid 6 through 138) selection = (chain 'K' and resid 6 through 138) selection = (chain 'L' and resid 6 through 138) selection = (chain 'M' and resid 6 through 138) selection = chain 'N' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.250 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.360 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.708 25766 Z= 0.716 Angle : 0.804 8.966 34967 Z= 0.522 Chirality : 0.053 0.381 4072 Planarity : 0.007 0.089 4279 Dihedral : 13.961 171.155 9936 Min Nonbonded Distance : 0.924 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.67 % Favored : 98.27 % Rotamer: Outliers : 0.34 % Allowed : 0.49 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 3062 helix: 1.65 (0.15), residues: 1265 sheet: 1.15 (0.19), residues: 629 loop : -0.95 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 13 TYR 0.109 0.004 TYR N 48 PHE 0.026 0.002 PHE M 22 TRP 0.006 0.001 TRP H 199 HIS 0.003 0.001 HIS E 55 Details of bonding type rmsd covalent geometry : bond 0.00635 (25764) covalent geometry : angle 0.80387 (34967) hydrogen bonds : bond 0.13189 ( 1071) hydrogen bonds : angle 5.28006 ( 3102) Misc. bond : bond 0.69968 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 856 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 16 ASN cc_start: 0.7940 (m-40) cc_final: 0.7479 (m-40) REVERT: I 22 PHE cc_start: 0.7454 (t80) cc_final: 0.7156 (t80) REVERT: I 49 ASP cc_start: 0.8695 (m-30) cc_final: 0.8491 (m-30) REVERT: I 67 THR cc_start: 0.6719 (p) cc_final: 0.6170 (t) REVERT: I 109 PHE cc_start: 0.8180 (t80) cc_final: 0.7969 (t80) REVERT: I 116 ASP cc_start: 0.7305 (t0) cc_final: 0.5808 (t0) REVERT: I 117 VAL cc_start: 0.7940 (OUTLIER) cc_final: 0.7529 (t) REVERT: I 119 TYR cc_start: 0.8602 (m-80) cc_final: 0.7351 (m-10) REVERT: I 121 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.8253 (mtp180) REVERT: I 132 ASN cc_start: 0.9138 (m-40) cc_final: 0.8627 (m110) REVERT: K 14 ILE cc_start: 0.9458 (mm) cc_final: 0.9227 (mm) REVERT: K 46 VAL cc_start: 0.8072 (t) cc_final: 0.7436 (t) REVERT: K 49 ASP cc_start: 0.8533 (m-30) cc_final: 0.8243 (p0) REVERT: K 56 MET cc_start: 0.8723 (mmm) cc_final: 0.8252 (mmm) REVERT: K 108 ASP cc_start: 0.8330 (m-30) cc_final: 0.8121 (m-30) REVERT: K 122 LYS cc_start: 0.8915 (tttt) cc_final: 0.8429 (mtmm) REVERT: K 138 SER cc_start: 0.8135 (t) cc_final: 0.7697 (p) REVERT: L 10 ILE cc_start: 0.8654 (mt) cc_final: 0.8318 (mm) REVERT: L 58 ILE cc_start: 0.9094 (mt) cc_final: 0.8868 (mm) REVERT: L 67 THR cc_start: 0.6100 (p) cc_final: 0.5795 (t) REVERT: L 82 TYR cc_start: 0.8028 (m-80) cc_final: 0.7756 (m-80) REVERT: L 87 VAL cc_start: 0.8840 (t) cc_final: 0.8543 (p) REVERT: L 121 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7931 (mtm180) REVERT: L 138 SER cc_start: 0.8875 (t) cc_final: 0.8550 (p) REVERT: M 11 ILE cc_start: 0.9210 (mt) cc_final: 0.8872 (tt) REVERT: M 20 VAL cc_start: 0.9028 (t) cc_final: 0.8768 (t) REVERT: M 58 ILE cc_start: 0.8848 (mt) cc_final: 0.8333 (mm) REVERT: M 85 VAL cc_start: 0.9110 (t) cc_final: 0.8783 (m) REVERT: M 96 VAL cc_start: 0.9160 (t) cc_final: 0.8652 (m) REVERT: N 10 ILE cc_start: 0.8543 (mt) cc_final: 0.8266 (tt) REVERT: N 36 ASN cc_start: 0.5560 (m-40) cc_final: 0.4842 (m110) REVERT: N 49 ASP cc_start: 0.8778 (m-30) cc_final: 0.8543 (p0) REVERT: N 58 ILE cc_start: 0.8565 (mt) cc_final: 0.8034 (mm) REVERT: N 87 VAL cc_start: 0.6494 (t) cc_final: 0.6225 (m) REVERT: N 112 MET cc_start: 0.7853 (mtp) cc_final: 0.7003 (mtp) REVERT: N 113 ILE cc_start: 0.8280 (mm) cc_final: 0.7881 (mm) REVERT: B 124 MET cc_start: 0.8511 (ttp) cc_final: 0.8015 (tmm) REVERT: C 262 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7601 (mp0) REVERT: D 300 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7526 (pp20) REVERT: A 44 TYR cc_start: 0.7256 (m-80) cc_final: 0.6923 (m-80) REVERT: A 124 MET cc_start: 0.8904 (ttp) cc_final: 0.8503 (ttt) REVERT: A 161 VAL cc_start: 0.8781 (t) cc_final: 0.8567 (m) REVERT: H 68 MET cc_start: 0.5547 (mmm) cc_final: 0.4084 (mtt) REVERT: H 173 PHE cc_start: 0.6518 (p90) cc_final: 0.6176 (p90) REVERT: H 239 PHE cc_start: 0.4962 (m-80) cc_final: 0.4465 (m-80) REVERT: F 13 GLU cc_start: 0.6335 (pm20) cc_final: 0.6044 (pm20) REVERT: F 57 TYR cc_start: 0.8196 (t80) cc_final: 0.7893 (t80) REVERT: F 115 ASP cc_start: 0.7542 (t0) cc_final: 0.7285 (t70) REVERT: F 184 TYR cc_start: 0.8449 (m-80) cc_final: 0.7742 (m-80) REVERT: F 248 MET cc_start: 0.9049 (mmm) cc_final: 0.8705 (mmm) REVERT: G 125 TYR cc_start: 0.8228 (t80) cc_final: 0.7526 (t80) REVERT: G 190 LEU cc_start: 0.9139 (tp) cc_final: 0.8819 (tp) outliers start: 8 outliers final: 1 residues processed: 859 average time/residue: 0.2614 time to fit residues: 330.6969 Evaluate side-chains 446 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 444 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain B residue 190 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.0370 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 10.0000 overall best weight: 2.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 ASN K 36 ASN K 104 GLN L 9 ASN ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN B 16 ASN A 11 ASN A 16 ASN H 11 HIS E 58 GLN F 58 GLN F 165 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.108587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.081248 restraints weight = 143277.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.084026 restraints weight = 52752.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.085701 restraints weight = 29449.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.086696 restraints weight = 20905.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.087227 restraints weight = 17187.132| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25766 Z= 0.182 Angle : 0.583 25.543 34967 Z= 0.307 Chirality : 0.054 1.427 4072 Planarity : 0.004 0.052 4279 Dihedral : 10.865 163.413 4068 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.12 % Favored : 97.84 % Rotamer: Outliers : 3.21 % Allowed : 11.56 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.15), residues: 3062 helix: 2.48 (0.15), residues: 1245 sheet: 1.22 (0.19), residues: 614 loop : -1.02 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 33 TYR 0.016 0.001 TYR L 48 PHE 0.019 0.001 PHE J 34 TRP 0.016 0.002 TRP H 12 HIS 0.008 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00402 (25764) covalent geometry : angle 0.58307 (34967) hydrogen bonds : bond 0.04110 ( 1071) hydrogen bonds : angle 4.10806 ( 3102) Misc. bond : bond 0.00159 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 439 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 135 LYS cc_start: 0.6620 (mttt) cc_final: 0.6266 (mmtt) REVERT: I 11 ILE cc_start: 0.8698 (mt) cc_final: 0.8457 (mm) REVERT: I 16 ASN cc_start: 0.8440 (m-40) cc_final: 0.8096 (m110) REVERT: I 49 ASP cc_start: 0.9314 (m-30) cc_final: 0.9024 (m-30) REVERT: I 94 TYR cc_start: 0.7413 (m-80) cc_final: 0.7150 (m-10) REVERT: I 111 ARG cc_start: 0.8671 (ttm110) cc_final: 0.8262 (mtt180) REVERT: I 116 ASP cc_start: 0.6142 (t0) cc_final: 0.5616 (t0) REVERT: I 119 TYR cc_start: 0.8223 (m-80) cc_final: 0.7551 (m-10) REVERT: I 121 ARG cc_start: 0.8860 (mtm-85) cc_final: 0.8012 (mtp-110) REVERT: I 128 MET cc_start: 0.8704 (mmm) cc_final: 0.8432 (mmm) REVERT: I 132 ASN cc_start: 0.9254 (m-40) cc_final: 0.8846 (m110) REVERT: K 18 LEU cc_start: 0.9365 (mm) cc_final: 0.9161 (mm) REVERT: K 49 ASP cc_start: 0.9085 (m-30) cc_final: 0.8837 (m-30) REVERT: K 108 ASP cc_start: 0.8256 (m-30) cc_final: 0.8035 (m-30) REVERT: K 119 TYR cc_start: 0.8468 (m-80) cc_final: 0.7753 (m-80) REVERT: K 122 LYS cc_start: 0.8840 (tttt) cc_final: 0.8494 (mtpt) REVERT: K 132 ASN cc_start: 0.8879 (m-40) cc_final: 0.8655 (m-40) REVERT: K 138 SER cc_start: 0.8352 (t) cc_final: 0.7913 (p) REVERT: L 24 TYR cc_start: 0.8676 (t80) cc_final: 0.7694 (t80) REVERT: L 67 THR cc_start: 0.5914 (p) cc_final: 0.5518 (t) REVERT: L 82 TYR cc_start: 0.8260 (m-80) cc_final: 0.7882 (m-80) REVERT: L 116 ASP cc_start: 0.8003 (t0) cc_final: 0.7725 (t0) REVERT: L 118 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: L 138 SER cc_start: 0.8890 (t) cc_final: 0.8481 (p) REVERT: M 11 ILE cc_start: 0.9056 (mt) cc_final: 0.8841 (tt) REVERT: M 34 PHE cc_start: 0.8244 (t80) cc_final: 0.8004 (t80) REVERT: M 59 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8484 (p0) REVERT: M 101 PRO cc_start: 0.8073 (Cg_endo) cc_final: 0.7672 (Cg_exo) REVERT: M 107 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7292 (pp20) REVERT: M 118 TYR cc_start: 0.7593 (t80) cc_final: 0.7356 (t80) REVERT: N 24 TYR cc_start: 0.7354 (t80) cc_final: 0.6873 (t80) REVERT: N 58 ILE cc_start: 0.8627 (mt) cc_final: 0.8230 (mt) REVERT: N 86 ASN cc_start: 0.7112 (m-40) cc_final: 0.6324 (p0) REVERT: N 109 PHE cc_start: 0.8576 (t80) cc_final: 0.8256 (t80) REVERT: B 124 MET cc_start: 0.8773 (ttp) cc_final: 0.7256 (tmm) REVERT: B 266 ASP cc_start: 0.7574 (m-30) cc_final: 0.7178 (p0) REVERT: C 262 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7798 (mp0) REVERT: D 149 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8443 (p0) REVERT: A 16 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8391 (t0) REVERT: A 124 MET cc_start: 0.8946 (ttp) cc_final: 0.8424 (ttt) REVERT: H 49 ASP cc_start: 0.4382 (m-30) cc_final: 0.3067 (p0) REVERT: H 68 MET cc_start: 0.5084 (mmm) cc_final: 0.3850 (mmm) REVERT: H 173 PHE cc_start: 0.6581 (p90) cc_final: 0.5937 (p90) REVERT: H 182 ARG cc_start: 0.6529 (tpm170) cc_final: 0.5938 (tpm170) REVERT: H 185 PHE cc_start: 0.6266 (m-10) cc_final: 0.6052 (m-10) REVERT: H 239 PHE cc_start: 0.4498 (m-80) cc_final: 0.4140 (m-80) REVERT: F 57 TYR cc_start: 0.8585 (t80) cc_final: 0.8364 (t80) REVERT: F 115 ASP cc_start: 0.7410 (t0) cc_final: 0.6926 (t0) REVERT: F 184 TYR cc_start: 0.8492 (m-80) cc_final: 0.7818 (m-80) REVERT: F 246 LYS cc_start: 0.9104 (tppt) cc_final: 0.8815 (tppt) REVERT: G 227 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8365 (t80) outliers start: 84 outliers final: 57 residues processed: 487 average time/residue: 0.2411 time to fit residues: 181.9178 Evaluate side-chains 450 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 387 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain L residue 118 TYR Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 ASP Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 132 ASN Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 227 TYR Chi-restraints excluded: chain G residue 285 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 236 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 209 optimal weight: 40.0000 chunk 220 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 104 GLN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN K 36 ASN ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN A 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.105805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.078125 restraints weight = 160599.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.081327 restraints weight = 59753.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.082218 restraints weight = 32944.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.082757 restraints weight = 24391.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.082953 restraints weight = 23010.940| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 25766 Z= 0.168 Angle : 0.558 35.947 34967 Z= 0.287 Chirality : 0.055 1.459 4072 Planarity : 0.003 0.047 4279 Dihedral : 10.768 151.580 4068 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.62 % Rotamer: Outliers : 3.25 % Allowed : 13.87 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.15), residues: 3062 helix: 2.48 (0.14), residues: 1257 sheet: 1.13 (0.20), residues: 607 loop : -1.06 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 33 TYR 0.019 0.001 TYR B 125 PHE 0.015 0.001 PHE J 34 TRP 0.007 0.001 TRP H 138 HIS 0.005 0.001 HIS D 27 Details of bonding type rmsd covalent geometry : bond 0.00376 (25764) covalent geometry : angle 0.55780 (34967) hydrogen bonds : bond 0.03768 ( 1071) hydrogen bonds : angle 3.86331 ( 3102) Misc. bond : bond 0.00130 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 388 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 135 LYS cc_start: 0.7116 (mttt) cc_final: 0.6879 (mmtt) REVERT: I 11 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8551 (mm) REVERT: I 16 ASN cc_start: 0.8675 (m-40) cc_final: 0.8356 (m110) REVERT: I 49 ASP cc_start: 0.9315 (m-30) cc_final: 0.8983 (m-30) REVERT: I 94 TYR cc_start: 0.7313 (m-80) cc_final: 0.6689 (m-10) REVERT: I 111 ARG cc_start: 0.8802 (ttm110) cc_final: 0.8378 (mtm-85) REVERT: I 115 GLU cc_start: 0.7887 (tt0) cc_final: 0.7480 (tt0) REVERT: I 116 ASP cc_start: 0.6854 (t0) cc_final: 0.6380 (t0) REVERT: I 119 TYR cc_start: 0.8198 (m-80) cc_final: 0.7411 (m-10) REVERT: I 121 ARG cc_start: 0.8912 (mtm-85) cc_final: 0.7943 (mtp-110) REVERT: I 128 MET cc_start: 0.8811 (mmm) cc_final: 0.8309 (mmm) REVERT: I 132 ASN cc_start: 0.9185 (m-40) cc_final: 0.8776 (m110) REVERT: K 18 LEU cc_start: 0.9381 (mm) cc_final: 0.9157 (mm) REVERT: K 49 ASP cc_start: 0.9086 (m-30) cc_final: 0.8821 (m-30) REVERT: K 108 ASP cc_start: 0.8313 (m-30) cc_final: 0.8079 (m-30) REVERT: K 122 LYS cc_start: 0.8880 (tttt) cc_final: 0.8571 (mtmt) REVERT: K 132 ASN cc_start: 0.8888 (m-40) cc_final: 0.8491 (m110) REVERT: K 138 SER cc_start: 0.8380 (t) cc_final: 0.7970 (p) REVERT: L 24 TYR cc_start: 0.8678 (t80) cc_final: 0.7783 (t80) REVERT: L 48 TYR cc_start: 0.8194 (t80) cc_final: 0.7973 (t80) REVERT: L 67 THR cc_start: 0.6196 (p) cc_final: 0.5771 (t) REVERT: L 116 ASP cc_start: 0.8058 (t0) cc_final: 0.7639 (t0) REVERT: L 118 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7464 (m-80) REVERT: L 138 SER cc_start: 0.8830 (t) cc_final: 0.8438 (p) REVERT: M 41 GLU cc_start: 0.7021 (tp30) cc_final: 0.6619 (tp30) REVERT: M 45 LYS cc_start: 0.8525 (mttt) cc_final: 0.8186 (mmmm) REVERT: M 59 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8327 (p0) REVERT: M 118 TYR cc_start: 0.7633 (t80) cc_final: 0.7363 (t80) REVERT: N 40 LYS cc_start: 0.6844 (pttt) cc_final: 0.6617 (pttt) REVERT: N 58 ILE cc_start: 0.8623 (mt) cc_final: 0.8375 (mt) REVERT: N 86 ASN cc_start: 0.7257 (m-40) cc_final: 0.6583 (p0) REVERT: B 124 MET cc_start: 0.8806 (ttp) cc_final: 0.7452 (tmm) REVERT: B 266 ASP cc_start: 0.7705 (m-30) cc_final: 0.7045 (p0) REVERT: C 262 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7828 (mp0) REVERT: C 275 MET cc_start: 0.8254 (tmm) cc_final: 0.7973 (tmm) REVERT: A 124 MET cc_start: 0.8841 (ttp) cc_final: 0.8231 (ttt) REVERT: H 68 MET cc_start: 0.5530 (mmm) cc_final: 0.4077 (mmm) REVERT: H 173 PHE cc_start: 0.6467 (p90) cc_final: 0.5730 (p90) REVERT: F 57 TYR cc_start: 0.8696 (t80) cc_final: 0.8492 (t80) REVERT: F 115 ASP cc_start: 0.7399 (t0) cc_final: 0.6876 (t0) REVERT: F 154 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7298 (tm-30) REVERT: F 184 TYR cc_start: 0.8556 (m-80) cc_final: 0.7794 (m-80) REVERT: G 124 MET cc_start: 0.6780 (ttt) cc_final: 0.6518 (ttt) REVERT: G 227 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8593 (t80) REVERT: G 296 ASN cc_start: 0.7711 (m-40) cc_final: 0.6943 (t0) outliers start: 85 outliers final: 61 residues processed: 430 average time/residue: 0.2409 time to fit residues: 159.6728 Evaluate side-chains 422 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 357 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 118 TYR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 ASP Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain M residue 121 ARG Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 132 ASN Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 227 TYR Chi-restraints excluded: chain G residue 285 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 167 optimal weight: 6.9990 chunk 264 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 222 optimal weight: 0.8980 chunk 217 optimal weight: 7.9990 chunk 253 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 300 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 20.0000 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN C 154 GLN ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.101022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.073422 restraints weight = 144541.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.075951 restraints weight = 55841.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.077494 restraints weight = 32582.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.078401 restraints weight = 23852.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.078913 restraints weight = 20017.768| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 25766 Z= 0.280 Angle : 0.677 20.973 34967 Z= 0.355 Chirality : 0.057 1.495 4072 Planarity : 0.005 0.071 4279 Dihedral : 11.183 130.506 4066 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 27.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.42 % Allowed : 15.19 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3062 helix: 1.73 (0.14), residues: 1264 sheet: 0.49 (0.21), residues: 606 loop : -1.29 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 133 TYR 0.020 0.002 TYR B 125 PHE 0.018 0.002 PHE H 173 TRP 0.011 0.002 TRP H 12 HIS 0.009 0.002 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00624 (25764) covalent geometry : angle 0.67743 (34967) hydrogen bonds : bond 0.04678 ( 1071) hydrogen bonds : angle 4.41771 ( 3102) Misc. bond : bond 0.00124 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 331 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 ARG cc_start: 0.8345 (mtp-110) cc_final: 0.8072 (mtp-110) REVERT: I 16 ASN cc_start: 0.8748 (m-40) cc_final: 0.8483 (m110) REVERT: I 30 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8655 (pp) REVERT: I 49 ASP cc_start: 0.9353 (m-30) cc_final: 0.9064 (m-30) REVERT: I 111 ARG cc_start: 0.8950 (ttm110) cc_final: 0.8460 (mtm-85) REVERT: I 112 MET cc_start: 0.7207 (mmm) cc_final: 0.6877 (ttm) REVERT: I 121 ARG cc_start: 0.8927 (mtm-85) cc_final: 0.7858 (mtp-110) REVERT: I 128 MET cc_start: 0.8894 (mmm) cc_final: 0.8507 (mmm) REVERT: I 132 ASN cc_start: 0.9218 (m-40) cc_final: 0.8944 (m110) REVERT: K 18 LEU cc_start: 0.9429 (mm) cc_final: 0.9177 (mm) REVERT: K 49 ASP cc_start: 0.9039 (m-30) cc_final: 0.8832 (m-30) REVERT: K 108 ASP cc_start: 0.8085 (m-30) cc_final: 0.7877 (m-30) REVERT: K 122 LYS cc_start: 0.8681 (tttt) cc_final: 0.8437 (mtmt) REVERT: K 128 MET cc_start: 0.8581 (tpp) cc_final: 0.8165 (tpp) REVERT: K 132 ASN cc_start: 0.9055 (m-40) cc_final: 0.8728 (m110) REVERT: K 138 SER cc_start: 0.8389 (t) cc_final: 0.7923 (p) REVERT: L 116 ASP cc_start: 0.8470 (t0) cc_final: 0.8085 (t0) REVERT: L 118 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7289 (m-80) REVERT: L 138 SER cc_start: 0.8715 (t) cc_final: 0.8341 (p) REVERT: M 41 GLU cc_start: 0.6840 (tp30) cc_final: 0.6333 (tp30) REVERT: M 59 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8147 (p0) REVERT: M 99 TYR cc_start: 0.7609 (m-80) cc_final: 0.7382 (m-80) REVERT: N 86 ASN cc_start: 0.7731 (m-40) cc_final: 0.7060 (p0) REVERT: B 112 MET cc_start: 0.8010 (ttm) cc_final: 0.7704 (mtt) REVERT: B 124 MET cc_start: 0.9201 (ttp) cc_final: 0.8340 (ttp) REVERT: C 275 MET cc_start: 0.8340 (tmm) cc_final: 0.8077 (tmm) REVERT: D 267 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8157 (t0) REVERT: A 124 MET cc_start: 0.8796 (ttp) cc_final: 0.8035 (ttt) REVERT: H 68 MET cc_start: 0.5982 (mmm) cc_final: 0.4375 (mmm) REVERT: H 173 PHE cc_start: 0.6785 (p90) cc_final: 0.5272 (p90) REVERT: E 13 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: F 124 MET cc_start: 0.8380 (ttt) cc_final: 0.7795 (ttp) REVERT: F 142 MET cc_start: 0.8784 (ttm) cc_final: 0.8475 (ttm) REVERT: F 154 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7761 (mm-40) REVERT: F 184 TYR cc_start: 0.8792 (m-80) cc_final: 0.8450 (m-80) REVERT: G 186 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8446 (p90) REVERT: G 296 ASN cc_start: 0.7724 (m-40) cc_final: 0.6914 (t0) outliers start: 116 outliers final: 85 residues processed: 406 average time/residue: 0.2196 time to fit residues: 140.1262 Evaluate side-chains 393 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 302 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 82 TYR Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 118 TYR Chi-restraints excluded: chain M residue 16 ASN Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 ASP Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain M residue 121 ARG Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 49 ASP Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 132 ASN Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 313 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain G residue 186 PHE Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 227 TYR Chi-restraints excluded: chain G residue 285 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 239 optimal weight: 0.0010 chunk 289 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.102936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.075859 restraints weight = 139637.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.078445 restraints weight = 53357.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.080015 restraints weight = 30563.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.080933 restraints weight = 22073.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.081377 restraints weight = 18402.299| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25766 Z= 0.110 Angle : 0.486 17.750 34967 Z= 0.261 Chirality : 0.055 1.449 4072 Planarity : 0.003 0.049 4279 Dihedral : 10.681 124.960 4066 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.68 % Allowed : 17.01 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.15), residues: 3062 helix: 2.43 (0.15), residues: 1264 sheet: 0.74 (0.21), residues: 594 loop : -1.12 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 132 TYR 0.014 0.001 TYR N 94 PHE 0.016 0.001 PHE K 109 TRP 0.012 0.001 TRP H 12 HIS 0.003 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00248 (25764) covalent geometry : angle 0.48644 (34967) hydrogen bonds : bond 0.03290 ( 1071) hydrogen bonds : angle 3.66010 ( 3102) Misc. bond : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 338 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 ARG cc_start: 0.8383 (mtp-110) cc_final: 0.8170 (mtp-110) REVERT: J 135 LYS cc_start: 0.6316 (mttt) cc_final: 0.5879 (mmtt) REVERT: I 16 ASN cc_start: 0.8737 (m-40) cc_final: 0.8467 (m110) REVERT: I 49 ASP cc_start: 0.9276 (m-30) cc_final: 0.8950 (m-30) REVERT: I 111 ARG cc_start: 0.8853 (ttm110) cc_final: 0.8418 (mtm-85) REVERT: I 121 ARG cc_start: 0.8931 (mtm-85) cc_final: 0.7915 (mtp-110) REVERT: I 132 ASN cc_start: 0.9215 (m-40) cc_final: 0.8811 (m110) REVERT: K 18 LEU cc_start: 0.9366 (mm) cc_final: 0.9145 (mm) REVERT: K 41 GLU cc_start: 0.8448 (mp0) cc_final: 0.8240 (pm20) REVERT: K 108 ASP cc_start: 0.8207 (m-30) cc_final: 0.7997 (m-30) REVERT: K 118 TYR cc_start: 0.7003 (t80) cc_final: 0.6735 (t80) REVERT: K 122 LYS cc_start: 0.8627 (tttt) cc_final: 0.8403 (mtmm) REVERT: K 138 SER cc_start: 0.8310 (t) cc_final: 0.7868 (p) REVERT: L 114 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8019 (pp20) REVERT: L 118 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7525 (m-80) REVERT: L 138 SER cc_start: 0.8594 (t) cc_final: 0.8269 (p) REVERT: M 41 GLU cc_start: 0.7235 (tp30) cc_final: 0.6844 (tp30) REVERT: M 59 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8123 (p0) REVERT: N 86 ASN cc_start: 0.7435 (m-40) cc_final: 0.6709 (p0) REVERT: N 99 TYR cc_start: 0.4904 (OUTLIER) cc_final: 0.4355 (t80) REVERT: B 124 MET cc_start: 0.9149 (ttp) cc_final: 0.8223 (ttp) REVERT: D 1 MET cc_start: 0.8049 (mtp) cc_final: 0.7842 (ttp) REVERT: D 267 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8236 (t0) REVERT: A 19 GLU cc_start: 0.7921 (tp30) cc_final: 0.7584 (tp30) REVERT: A 124 MET cc_start: 0.8679 (ttp) cc_final: 0.7882 (ttt) REVERT: H 68 MET cc_start: 0.5998 (mmm) cc_final: 0.4415 (mmm) REVERT: H 173 PHE cc_start: 0.6785 (p90) cc_final: 0.5525 (p90) REVERT: E 13 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7680 (pm20) REVERT: F 1 MET cc_start: 0.8142 (mtp) cc_final: 0.7683 (ttm) REVERT: F 124 MET cc_start: 0.8260 (ttt) cc_final: 0.7868 (ttp) REVERT: F 142 MET cc_start: 0.8757 (ttm) cc_final: 0.8458 (ttm) REVERT: F 154 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7385 (tm-30) REVERT: F 184 TYR cc_start: 0.8668 (m-80) cc_final: 0.8374 (m-80) REVERT: G 137 ILE cc_start: 0.9437 (pt) cc_final: 0.9088 (mt) REVERT: G 227 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8416 (t80) REVERT: G 296 ASN cc_start: 0.7688 (m-40) cc_final: 0.6875 (t0) outliers start: 70 outliers final: 53 residues processed: 378 average time/residue: 0.2388 time to fit residues: 140.3414 Evaluate side-chains 386 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 326 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 118 TYR Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 ASP Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain M residue 121 ARG Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 99 TYR Chi-restraints excluded: chain N residue 132 ASN Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 227 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 273 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 291 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 285 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 270 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN G 27 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.099805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.072401 restraints weight = 149642.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.074932 restraints weight = 56847.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.076470 restraints weight = 32833.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.077364 restraints weight = 23895.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.077809 restraints weight = 20035.926| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.6367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25766 Z= 0.294 Angle : 0.655 18.023 34967 Z= 0.346 Chirality : 0.057 1.494 4072 Planarity : 0.004 0.058 4279 Dihedral : 11.064 132.604 4066 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 29.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.23 % Allowed : 16.97 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3062 helix: 1.72 (0.14), residues: 1269 sheet: 0.13 (0.21), residues: 608 loop : -1.33 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 60 TYR 0.018 0.002 TYR A 79 PHE 0.017 0.002 PHE D 107 TRP 0.005 0.001 TRP H 138 HIS 0.009 0.002 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00648 (25764) covalent geometry : angle 0.65457 (34967) hydrogen bonds : bond 0.04490 ( 1071) hydrogen bonds : angle 4.41641 ( 3102) Misc. bond : bond 0.00106 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 310 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 ARG cc_start: 0.8410 (mtp-110) cc_final: 0.8198 (mtp-110) REVERT: J 135 LYS cc_start: 0.6295 (mttt) cc_final: 0.5842 (mmtt) REVERT: I 16 ASN cc_start: 0.8790 (m-40) cc_final: 0.8558 (m110) REVERT: I 29 THR cc_start: 0.8834 (m) cc_final: 0.8625 (m) REVERT: I 30 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8623 (pp) REVERT: I 41 GLU cc_start: 0.8630 (mp0) cc_final: 0.8377 (mp0) REVERT: I 49 ASP cc_start: 0.9367 (m-30) cc_final: 0.9122 (m-30) REVERT: I 121 ARG cc_start: 0.9087 (mtm-85) cc_final: 0.8875 (mtt90) REVERT: I 132 ASN cc_start: 0.9171 (m-40) cc_final: 0.8752 (m110) REVERT: K 18 LEU cc_start: 0.9447 (mm) cc_final: 0.9220 (mm) REVERT: K 122 LYS cc_start: 0.8903 (tttt) cc_final: 0.8509 (mtmt) REVERT: K 138 SER cc_start: 0.8363 (t) cc_final: 0.7911 (p) REVERT: L 118 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: L 138 SER cc_start: 0.8586 (t) cc_final: 0.8101 (p) REVERT: M 41 GLU cc_start: 0.6915 (tp30) cc_final: 0.6348 (tp30) REVERT: N 86 ASN cc_start: 0.7904 (m-40) cc_final: 0.7257 (p0) REVERT: N 99 TYR cc_start: 0.4840 (OUTLIER) cc_final: 0.4366 (t80) REVERT: B 112 MET cc_start: 0.8058 (ttm) cc_final: 0.7819 (mtt) REVERT: B 124 MET cc_start: 0.9167 (ttp) cc_final: 0.8355 (ttp) REVERT: D 267 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8211 (t0) REVERT: A 124 MET cc_start: 0.8753 (ttp) cc_final: 0.8022 (ttt) REVERT: E 13 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7471 (pm20) REVERT: F 13 GLU cc_start: 0.7007 (pm20) cc_final: 0.6655 (pm20) REVERT: F 124 MET cc_start: 0.8513 (ttt) cc_final: 0.8008 (ttp) REVERT: F 142 MET cc_start: 0.8747 (ttm) cc_final: 0.8497 (ttm) REVERT: F 154 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7810 (mm-40) REVERT: F 184 TYR cc_start: 0.8749 (m-80) cc_final: 0.8399 (m-80) REVERT: G 137 ILE cc_start: 0.9426 (pt) cc_final: 0.9120 (mt) REVERT: G 186 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8463 (p90) REVERT: G 296 ASN cc_start: 0.7779 (m-40) cc_final: 0.7045 (t0) outliers start: 111 outliers final: 86 residues processed: 383 average time/residue: 0.2253 time to fit residues: 135.7115 Evaluate side-chains 386 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 294 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 133 ARG Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 118 TYR Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 ASP Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain M residue 121 ARG Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 49 ASP Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 99 TYR Chi-restraints excluded: chain N residue 132 ASN Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain G residue 186 PHE Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 227 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 263 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 287 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 291 optimal weight: 8.9990 chunk 180 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 20.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.101597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.074328 restraints weight = 145036.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.076897 restraints weight = 55186.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.078469 restraints weight = 31886.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.079350 restraints weight = 23243.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.079902 restraints weight = 19525.655| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.6389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25766 Z= 0.124 Angle : 0.499 17.842 34967 Z= 0.267 Chirality : 0.055 1.461 4072 Planarity : 0.003 0.066 4279 Dihedral : 10.696 131.711 4066 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.06 % Allowed : 18.10 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 3062 helix: 2.31 (0.15), residues: 1264 sheet: 0.32 (0.21), residues: 608 loop : -1.23 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 133 TYR 0.014 0.001 TYR B 125 PHE 0.009 0.001 PHE E 159 TRP 0.011 0.001 TRP H 12 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00278 (25764) covalent geometry : angle 0.49859 (34967) hydrogen bonds : bond 0.03410 ( 1071) hydrogen bonds : angle 3.78394 ( 3102) Misc. bond : bond 0.00027 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 319 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 ARG cc_start: 0.8439 (mtp-110) cc_final: 0.8186 (ttm110) REVERT: J 135 LYS cc_start: 0.6696 (mttt) cc_final: 0.6302 (mmtt) REVERT: I 16 ASN cc_start: 0.8765 (m-40) cc_final: 0.8553 (m110) REVERT: I 41 GLU cc_start: 0.8761 (mp0) cc_final: 0.8460 (mp0) REVERT: I 49 ASP cc_start: 0.9251 (m-30) cc_final: 0.8922 (m-30) REVERT: I 132 ASN cc_start: 0.9156 (m-40) cc_final: 0.8718 (m110) REVERT: K 18 LEU cc_start: 0.9382 (mm) cc_final: 0.9161 (mm) REVERT: K 122 LYS cc_start: 0.8745 (tttt) cc_final: 0.8383 (mtmt) REVERT: K 138 SER cc_start: 0.8381 (t) cc_final: 0.7938 (p) REVERT: L 114 GLU cc_start: 0.8317 (pt0) cc_final: 0.7988 (pp20) REVERT: L 118 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.7332 (m-80) REVERT: L 138 SER cc_start: 0.8535 (t) cc_final: 0.8138 (p) REVERT: M 41 GLU cc_start: 0.6703 (tp30) cc_final: 0.6332 (tp30) REVERT: M 59 ASP cc_start: 0.8475 (p0) cc_final: 0.7863 (p0) REVERT: N 86 ASN cc_start: 0.8103 (m-40) cc_final: 0.7430 (p0) REVERT: N 99 TYR cc_start: 0.4689 (OUTLIER) cc_final: 0.4276 (t80) REVERT: B 112 MET cc_start: 0.7921 (ttm) cc_final: 0.7623 (mtt) REVERT: B 124 MET cc_start: 0.9152 (ttp) cc_final: 0.8282 (ttp) REVERT: D 267 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8318 (t0) REVERT: A 124 MET cc_start: 0.8678 (ttp) cc_final: 0.7931 (ttt) REVERT: H 68 MET cc_start: 0.6054 (mmm) cc_final: 0.4935 (mmm) REVERT: E 13 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: F 124 MET cc_start: 0.8334 (ttt) cc_final: 0.7907 (ttp) REVERT: F 142 MET cc_start: 0.8751 (ttm) cc_final: 0.8514 (ttm) REVERT: F 154 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7506 (tm-30) REVERT: F 184 TYR cc_start: 0.8715 (m-80) cc_final: 0.8359 (m-80) REVERT: G 137 ILE cc_start: 0.9371 (pt) cc_final: 0.9064 (mt) REVERT: G 296 ASN cc_start: 0.7737 (m-40) cc_final: 0.6901 (t0) outliers start: 80 outliers final: 72 residues processed: 370 average time/residue: 0.2217 time to fit residues: 129.3683 Evaluate side-chains 384 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 308 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 118 TYR Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 ASP Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain M residue 121 ARG Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 99 TYR Chi-restraints excluded: chain N residue 132 ASN Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 227 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 90 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 276 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.101936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.074542 restraints weight = 158398.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.077204 restraints weight = 57746.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.078859 restraints weight = 32683.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.079720 restraints weight = 23419.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.080317 restraints weight = 19630.247| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.6480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25766 Z= 0.116 Angle : 0.485 17.871 34967 Z= 0.258 Chirality : 0.054 1.467 4072 Planarity : 0.003 0.068 4279 Dihedral : 10.475 132.675 4066 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.10 % Allowed : 18.29 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.16), residues: 3062 helix: 2.64 (0.15), residues: 1264 sheet: 0.35 (0.21), residues: 610 loop : -1.11 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 133 TYR 0.012 0.001 TYR M 48 PHE 0.012 0.001 PHE N 109 TRP 0.008 0.001 TRP H 12 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00262 (25764) covalent geometry : angle 0.48491 (34967) hydrogen bonds : bond 0.03101 ( 1071) hydrogen bonds : angle 3.58516 ( 3102) Misc. bond : bond 0.00016 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 325 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 128 MET cc_start: 0.7585 (ttt) cc_final: 0.7264 (tmm) REVERT: J 133 ARG cc_start: 0.8461 (mtp-110) cc_final: 0.8215 (ttm110) REVERT: J 135 LYS cc_start: 0.6699 (mttt) cc_final: 0.6294 (mmtt) REVERT: I 30 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8608 (pp) REVERT: I 41 GLU cc_start: 0.8773 (mp0) cc_final: 0.8488 (mp0) REVERT: I 45 LYS cc_start: 0.8916 (mmmm) cc_final: 0.8333 (mmmm) REVERT: I 49 ASP cc_start: 0.9223 (m-30) cc_final: 0.8864 (m-30) REVERT: I 121 ARG cc_start: 0.9023 (mtt90) cc_final: 0.8166 (mtp-110) REVERT: I 132 ASN cc_start: 0.9166 (m-40) cc_final: 0.8745 (m110) REVERT: K 18 LEU cc_start: 0.9357 (mm) cc_final: 0.9147 (mm) REVERT: K 118 TYR cc_start: 0.7060 (t80) cc_final: 0.6807 (t80) REVERT: K 122 LYS cc_start: 0.8719 (tttt) cc_final: 0.8374 (mtmt) REVERT: K 138 SER cc_start: 0.8246 (t) cc_final: 0.7794 (p) REVERT: L 118 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: L 138 SER cc_start: 0.8443 (t) cc_final: 0.8060 (p) REVERT: M 41 GLU cc_start: 0.6579 (tp30) cc_final: 0.6193 (tp30) REVERT: M 59 ASP cc_start: 0.8347 (p0) cc_final: 0.7832 (p0) REVERT: N 86 ASN cc_start: 0.8108 (m-40) cc_final: 0.7485 (p0) REVERT: N 99 TYR cc_start: 0.5067 (OUTLIER) cc_final: 0.4753 (t80) REVERT: N 108 ASP cc_start: 0.8526 (m-30) cc_final: 0.8018 (m-30) REVERT: B 112 MET cc_start: 0.7919 (ttm) cc_final: 0.7596 (mtt) REVERT: B 124 MET cc_start: 0.9041 (ttp) cc_final: 0.8170 (tmm) REVERT: D 1 MET cc_start: 0.7861 (mtp) cc_final: 0.7659 (ttp) REVERT: D 267 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8263 (t0) REVERT: A 124 MET cc_start: 0.8666 (ttp) cc_final: 0.7914 (ttt) REVERT: E 13 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: F 124 MET cc_start: 0.8369 (ttt) cc_final: 0.7984 (ttp) REVERT: F 142 MET cc_start: 0.8725 (ttm) cc_final: 0.8485 (ttm) REVERT: F 154 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7565 (tm-30) REVERT: F 184 TYR cc_start: 0.8688 (m-80) cc_final: 0.8358 (m-80) REVERT: G 137 ILE cc_start: 0.9347 (pt) cc_final: 0.9059 (mt) REVERT: G 296 ASN cc_start: 0.7674 (m-40) cc_final: 0.6979 (t0) outliers start: 81 outliers final: 73 residues processed: 378 average time/residue: 0.2231 time to fit residues: 133.3221 Evaluate side-chains 384 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 306 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 118 TYR Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 32 ASP Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 99 TYR Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain M residue 121 ARG Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 99 TYR Chi-restraints excluded: chain N residue 132 ASN Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain G residue 227 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 166 optimal weight: 3.9990 chunk 234 optimal weight: 0.5980 chunk 167 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 127 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 51 GLN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 ASN ** 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 = 0.3777 r_free = 0.3777 target = 0.100814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.073455 restraints weight = 157444.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.076069 restraints weight = 57625.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.077666 restraints weight = 32673.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.078518 restraints weight = 23561.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.079115 restraints weight = 19779.008| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25766 Z= 0.170 Angle : 0.531 18.096 34967 Z= 0.281 Chirality : 0.055 1.481 4072 Planarity : 0.003 0.067 4279 Dihedral : 10.586 136.724 4065 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 27.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.44 % Allowed : 18.33 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.15), residues: 3062 helix: 2.48 (0.14), residues: 1264 sheet: 0.22 (0.21), residues: 607 loop : -1.12 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 133 TYR 0.014 0.001 TYR B 125 PHE 0.032 0.001 PHE E 175 TRP 0.004 0.001 TRP H 138 HIS 0.005 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00380 (25764) covalent geometry : angle 0.53102 (34967) hydrogen bonds : bond 0.03482 ( 1071) hydrogen bonds : angle 3.76705 ( 3102) Misc. bond : bond 0.00049 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 299 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 ARG cc_start: 0.8496 (mtp-110) cc_final: 0.8240 (ttm110) REVERT: J 135 LYS cc_start: 0.6811 (mttt) cc_final: 0.6404 (mmtt) REVERT: I 30 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8655 (pp) REVERT: I 41 GLU cc_start: 0.8799 (mp0) cc_final: 0.8476 (mp0) REVERT: I 45 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8377 (mmmm) REVERT: I 49 ASP cc_start: 0.9261 (m-30) cc_final: 0.8919 (m-30) REVERT: I 121 ARG cc_start: 0.9025 (mtt90) cc_final: 0.8690 (mtm-85) REVERT: I 132 ASN cc_start: 0.9170 (m-40) cc_final: 0.8742 (m110) REVERT: K 18 LEU cc_start: 0.9391 (mm) cc_final: 0.9183 (mm) REVERT: K 41 GLU cc_start: 0.8318 (pm20) cc_final: 0.7945 (mt-10) REVERT: K 122 LYS cc_start: 0.8801 (tttt) cc_final: 0.8403 (mtmt) REVERT: K 138 SER cc_start: 0.8274 (t) cc_final: 0.7836 (p) REVERT: L 118 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: L 138 SER cc_start: 0.8396 (t) cc_final: 0.7998 (p) REVERT: M 41 GLU cc_start: 0.6630 (tp30) cc_final: 0.6181 (tp30) REVERT: M 59 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7912 (p0) REVERT: N 86 ASN cc_start: 0.8082 (m-40) cc_final: 0.7311 (p0) REVERT: N 99 TYR cc_start: 0.5094 (OUTLIER) cc_final: 0.4866 (t80) REVERT: N 108 ASP cc_start: 0.8557 (m-30) cc_final: 0.8048 (m-30) REVERT: B 112 MET cc_start: 0.7990 (ttm) cc_final: 0.7735 (mtt) REVERT: B 124 MET cc_start: 0.9067 (ttp) cc_final: 0.8171 (ttp) REVERT: D 267 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8244 (t0) REVERT: A 1 MET cc_start: 0.7578 (ttp) cc_final: 0.6915 (ttp) REVERT: A 124 MET cc_start: 0.8701 (ttp) cc_final: 0.7958 (ttt) REVERT: E 13 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: E 124 MET cc_start: 0.6925 (ptm) cc_final: 0.6547 (ptm) REVERT: F 13 GLU cc_start: 0.7000 (pm20) cc_final: 0.6719 (pm20) REVERT: F 124 MET cc_start: 0.8508 (ttt) cc_final: 0.8137 (ttp) REVERT: F 142 MET cc_start: 0.8735 (ttm) cc_final: 0.8454 (ttm) REVERT: F 154 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7613 (tm-30) REVERT: F 184 TYR cc_start: 0.8779 (m-80) cc_final: 0.8370 (m-10) REVERT: G 137 ILE cc_start: 0.9347 (pt) cc_final: 0.9065 (mt) REVERT: G 296 ASN cc_start: 0.7711 (m-40) cc_final: 0.7096 (t0) outliers start: 90 outliers final: 81 residues processed: 364 average time/residue: 0.2085 time to fit residues: 121.0539 Evaluate side-chains 379 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 292 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 118 TYR Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 32 ASP Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 99 TYR Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain M residue 121 ARG Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 99 TYR Chi-restraints excluded: chain N residue 132 ASN Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain G residue 227 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 7 optimal weight: 20.0000 chunk 247 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 12 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.101567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.074161 restraints weight = 162628.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.076828 restraints weight = 59071.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.078478 restraints weight = 33181.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.079419 restraints weight = 23786.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.079869 restraints weight = 19760.365| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25766 Z= 0.120 Angle : 0.493 17.778 34967 Z= 0.262 Chirality : 0.055 1.457 4072 Planarity : 0.003 0.061 4279 Dihedral : 10.465 138.333 4065 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.14 % Allowed : 18.78 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.16), residues: 3062 helix: 2.66 (0.15), residues: 1264 sheet: 0.28 (0.21), residues: 607 loop : -1.07 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 133 TYR 0.014 0.001 TYR H 42 PHE 0.022 0.001 PHE E 175 TRP 0.010 0.001 TRP H 12 HIS 0.004 0.001 HIS F 55 Details of bonding type rmsd covalent geometry : bond 0.00272 (25764) covalent geometry : angle 0.49253 (34967) hydrogen bonds : bond 0.03121 ( 1071) hydrogen bonds : angle 3.56989 ( 3102) Misc. bond : bond 0.00015 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 309 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 ARG cc_start: 0.8497 (mtp-110) cc_final: 0.8224 (ttm110) REVERT: I 16 ASN cc_start: 0.8670 (m-40) cc_final: 0.7811 (p0) REVERT: I 41 GLU cc_start: 0.8732 (mp0) cc_final: 0.8365 (mp0) REVERT: I 45 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8357 (mmmm) REVERT: I 49 ASP cc_start: 0.9238 (m-30) cc_final: 0.8888 (m-30) REVERT: I 121 ARG cc_start: 0.9008 (mtt90) cc_final: 0.8398 (mtp-110) REVERT: I 132 ASN cc_start: 0.9100 (m-40) cc_final: 0.8642 (m110) REVERT: K 18 LEU cc_start: 0.9358 (mm) cc_final: 0.9152 (mm) REVERT: K 41 GLU cc_start: 0.8311 (pm20) cc_final: 0.7940 (mt-10) REVERT: K 118 TYR cc_start: 0.7104 (t80) cc_final: 0.6726 (t80) REVERT: K 122 LYS cc_start: 0.8717 (tttt) cc_final: 0.8351 (mtmt) REVERT: K 138 SER cc_start: 0.8253 (t) cc_final: 0.7820 (p) REVERT: L 118 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7449 (m-80) REVERT: L 138 SER cc_start: 0.8376 (t) cc_final: 0.7981 (p) REVERT: M 41 GLU cc_start: 0.6619 (tp30) cc_final: 0.6225 (tp30) REVERT: M 59 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.7964 (p0) REVERT: N 86 ASN cc_start: 0.8061 (m-40) cc_final: 0.7302 (p0) REVERT: N 108 ASP cc_start: 0.8544 (m-30) cc_final: 0.8007 (m-30) REVERT: B 112 MET cc_start: 0.7958 (ttm) cc_final: 0.7695 (mtt) REVERT: B 124 MET cc_start: 0.9046 (ttp) cc_final: 0.8163 (ttp) REVERT: A 124 MET cc_start: 0.8690 (ttp) cc_final: 0.7943 (ttt) REVERT: E 13 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: E 124 MET cc_start: 0.6976 (ptm) cc_final: 0.6504 (ptm) REVERT: F 13 GLU cc_start: 0.6946 (pm20) cc_final: 0.6654 (pm20) REVERT: F 142 MET cc_start: 0.8723 (ttm) cc_final: 0.8435 (ttm) REVERT: F 154 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7548 (tm-30) REVERT: F 184 TYR cc_start: 0.8772 (m-80) cc_final: 0.8341 (m-10) REVERT: G 137 ILE cc_start: 0.9334 (pt) cc_final: 0.9055 (mt) REVERT: G 296 ASN cc_start: 0.7725 (m-40) cc_final: 0.7111 (t0) outliers start: 82 outliers final: 74 residues processed: 366 average time/residue: 0.2467 time to fit residues: 143.1706 Evaluate side-chains 380 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 303 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 118 TYR Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 32 ASP Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 99 TYR Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 132 ASN Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain G residue 227 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 167 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 189 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 6 optimal weight: 0.0060 chunk 160 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 259 optimal weight: 6.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN F 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.101535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.074388 restraints weight = 152846.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.077005 restraints weight = 56575.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.078593 restraints weight = 32161.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.079519 restraints weight = 23229.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.079955 restraints weight = 19362.696| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.6802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25766 Z= 0.121 Angle : 0.492 17.843 34967 Z= 0.261 Chirality : 0.055 1.463 4072 Planarity : 0.003 0.051 4279 Dihedral : 10.420 140.971 4065 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 27.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.17 % Allowed : 18.90 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.16), residues: 3062 helix: 2.71 (0.15), residues: 1264 sheet: 0.28 (0.21), residues: 607 loop : -1.07 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 133 TYR 0.014 0.001 TYR H 42 PHE 0.023 0.001 PHE E 175 TRP 0.007 0.001 TRP H 12 HIS 0.004 0.001 HIS F 55 Details of bonding type rmsd covalent geometry : bond 0.00274 (25764) covalent geometry : angle 0.49202 (34967) hydrogen bonds : bond 0.03084 ( 1071) hydrogen bonds : angle 3.53451 ( 3102) Misc. bond : bond 0.00011 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7654.55 seconds wall clock time: 131 minutes 35.83 seconds (7895.83 seconds total)