Starting phenix.real_space_refine on Mon Jul 6 08:20:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cro_45873/07_2026/9cro_45873_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cro_45873/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cro_45873/07_2026/9cro_45873_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cro_45873/07_2026/9cro_45873_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cro_45873/07_2026/9cro_45873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cro_45873/07_2026/9cro_45873.map" } 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-dev-6108/lib/python3.11/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: 6.17, per 1000 atoms: 0.19 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: 2.35 Conformation dependent library (CDL) restraints added in 930.6 milliseconds 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: 3.97 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: 6.56 Time building geometry restraints manager: 3.19 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.310 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 30.800 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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= 0.717 Angle : 0.804 8.966 34967 Z= 0.526 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/Z covalent geometry : bond 0.00636 / 0.37 (25764) covalent geometry : angle 0.80386 / 0.53 (34967) hydrogen bonds : bond 0.13189 / 8.78 ( 1071) hydrogen bonds : angle 5.28006 / 3.77 ( 3102) Misc. bond : bond 0.69968 / 35.16 ( 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 : 0.884 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: 0.2713 time to fit residues: 344.9029 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 : 1.072 ------------------------------------------------------------------------------- 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... ** J 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN K 16 ASN K 36 ASN K 104 GLN L 9 ASN ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN C 16 ASN D 58 GLN A 11 ASN H 11 HIS ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN F 58 GLN F 165 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.111236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.084136 restraints weight = 141947.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.086985 restraints weight = 51729.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.088731 restraints weight = 28706.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.089651 restraints weight = 20243.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.090288 restraints weight = 16760.803| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25766 Z= 0.192 Angle : 0.597 18.990 34967 Z= 0.317 Chirality : 0.055 1.457 4072 Planarity : 0.004 0.061 4279 Dihedral : 11.023 165.819 4068 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 3.55 % Allowed : 10.85 % Favored : 85.60 % 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: 1.31 (0.15), residues: 3062 helix: 2.42 (0.15), residues: 1244 sheet: 1.21 (0.19), residues: 615 loop : -1.05 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 133 TYR 0.026 0.002 TYR L 48 PHE 0.027 0.001 PHE J 34 TRP 0.016 0.002 TRP H 12 HIS 0.020 0.002 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (25764) covalent geometry : angle 0.59746 / 0.32 (34967) hydrogen bonds : bond 0.04582 / 3.05 ( 1071) hydrogen bonds : angle 4.24493 / 3.04 ( 3102) Misc. bond : bond 0.01415 / 0.69 ( 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 514 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 421 time to evaluate : 1.127 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: J 55 GLN cc_start: 0.4089 (mm-40) cc_final: 0.3865 (mm-40) REVERT: J 128 MET cc_start: 0.8058 (ttm) cc_final: 0.7857 (ttt) REVERT: J 135 LYS cc_start: 0.6304 (mttt) cc_final: 0.5902 (mmtt) REVERT: I 16 ASN cc_start: 0.8339 (m-40) cc_final: 0.8041 (m-40) REVERT: I 49 ASP cc_start: 0.9205 (m-30) cc_final: 0.8798 (m-30) REVERT: I 94 TYR cc_start: 0.7632 (m-80) cc_final: 0.7301 (m-10) REVERT: I 111 ARG cc_start: 0.8658 (ttm110) cc_final: 0.8197 (mtt180) REVERT: I 112 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6922 (mtm) REVERT: I 119 TYR cc_start: 0.8213 (m-80) cc_final: 0.7951 (m-10) REVERT: I 121 ARG cc_start: 0.8875 (mtm-85) cc_final: 0.8317 (mtp180) REVERT: I 132 ASN cc_start: 0.9237 (m-40) cc_final: 0.8955 (m-40) REVERT: K 18 LEU cc_start: 0.9378 (mm) cc_final: 0.9126 (mm) REVERT: K 36 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7944 (m110) REVERT: K 49 ASP cc_start: 0.8936 (m-30) cc_final: 0.8660 (m-30) REVERT: K 119 TYR cc_start: 0.8412 (m-80) cc_final: 0.7938 (m-80) REVERT: K 122 LYS cc_start: 0.8681 (tttt) cc_final: 0.8393 (mtpt) REVERT: K 138 SER cc_start: 0.8377 (t) cc_final: 0.7960 (p) REVERT: L 24 TYR cc_start: 0.8467 (t80) cc_final: 0.7653 (t80) REVERT: L 82 TYR cc_start: 0.7992 (m-80) cc_final: 0.7618 (m-80) REVERT: L 118 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: L 138 SER cc_start: 0.9037 (t) cc_final: 0.8710 (p) REVERT: M 11 ILE cc_start: 0.9092 (mt) cc_final: 0.8847 (tt) REVERT: M 45 LYS cc_start: 0.8475 (mttt) cc_final: 0.8236 (mmmm) REVERT: M 107 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7321 (pp20) REVERT: N 24 TYR cc_start: 0.7447 (t80) cc_final: 0.6998 (t80) REVERT: N 49 ASP cc_start: 0.9047 (m-30) cc_final: 0.8417 (p0) REVERT: N 58 ILE cc_start: 0.8523 (mt) cc_final: 0.8129 (mt) REVERT: N 109 PHE cc_start: 0.8595 (t80) cc_final: 0.8179 (t80) REVERT: B 124 MET cc_start: 0.8694 (ttp) cc_final: 0.7120 (tmm) REVERT: C 262 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7787 (mp0) REVERT: A 124 MET cc_start: 0.8868 (ttp) cc_final: 0.8408 (ttt) REVERT: H 68 MET cc_start: 0.5317 (mmm) cc_final: 0.4010 (mmm) REVERT: H 173 PHE cc_start: 0.6402 (p90) cc_final: 0.5877 (p90) REVERT: H 239 PHE cc_start: 0.4515 (m-80) cc_final: 0.4314 (m-80) REVERT: F 13 GLU cc_start: 0.6334 (pm20) cc_final: 0.5982 (pm20) REVERT: F 57 TYR cc_start: 0.8490 (t80) cc_final: 0.8246 (t80) REVERT: F 115 ASP cc_start: 0.7339 (t0) cc_final: 0.6818 (t0) REVERT: F 184 TYR cc_start: 0.8451 (m-80) cc_final: 0.7794 (m-80) REVERT: G 313 ASP cc_start: 0.8598 (m-30) cc_final: 0.8341 (t0) outliers start: 93 outliers final: 68 residues processed: 469 average time/residue: 0.2315 time to fit residues: 169.2142 Evaluate side-chains 450 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 378 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 18 LEU Chi-restraints excluded: chain I residue 58 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 112 MET Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 113 ILE 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 39 SER Chi-restraints excluded: chain M residue 56 MET 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 M residue 121 ARG Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 85 VAL 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 308 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain C residue 1 MET 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 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 250 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 275 MET 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 82 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 34 LEU 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 F residue 311 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 201 PHE 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: 1.9990 chunk 157 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 209 optimal weight: 40.0000 chunk 220 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 42 optimal weight: 0.3980 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 104 GLN ** J 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN C 16 ASN A 16 ASN G 214 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.109265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.081820 restraints weight = 155554.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.084694 restraints weight = 55126.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.086465 restraints weight = 30194.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.087490 restraints weight = 21171.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.087993 restraints weight = 17349.293| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25766 Z= 0.158 Angle : 0.525 23.738 34967 Z= 0.280 Chirality : 0.055 1.479 4072 Planarity : 0.003 0.044 4279 Dihedral : 10.821 162.763 4067 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.81 % Rotamer: Outliers : 3.10 % Allowed : 13.19 % Favored : 83.71 % 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: 1.41 (0.15), residues: 3062 helix: 2.58 (0.15), residues: 1250 sheet: 1.13 (0.20), residues: 616 loop : -1.03 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 60 TYR 0.018 0.001 TYR I 94 PHE 0.013 0.001 PHE J 34 TRP 0.010 0.002 TRP H 12 HIS 0.009 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (25764) covalent geometry : angle 0.52521 / 0.28 (34967) hydrogen bonds : bond 0.04036 / 2.68 ( 1071) hydrogen bonds : angle 3.96894 / 2.83 ( 3102) Misc. bond : bond 0.01135 / 0.54 ( 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 477 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 396 time to evaluate : 1.133 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: J 135 LYS cc_start: 0.6749 (mttt) cc_final: 0.6515 (mmtt) REVERT: I 16 ASN cc_start: 0.8368 (m-40) cc_final: 0.8045 (m110) REVERT: I 49 ASP cc_start: 0.9262 (m-30) cc_final: 0.8877 (m-30) REVERT: I 111 ARG cc_start: 0.8674 (ttm110) cc_final: 0.8253 (mtt180) REVERT: I 112 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6767 (mtm) REVERT: I 121 ARG cc_start: 0.8811 (mtm-85) cc_final: 0.8172 (mtp-110) REVERT: I 132 ASN cc_start: 0.9263 (m-40) cc_final: 0.8986 (m-40) REVERT: K 18 LEU cc_start: 0.9400 (mm) cc_final: 0.9178 (mm) REVERT: K 36 ASN cc_start: 0.8663 (t0) cc_final: 0.8375 (m110) REVERT: K 49 ASP cc_start: 0.9055 (m-30) cc_final: 0.8792 (m-30) REVERT: K 122 LYS cc_start: 0.8722 (tttt) cc_final: 0.8455 (mtmt) REVERT: K 132 ASN cc_start: 0.8763 (m-40) cc_final: 0.8561 (m-40) REVERT: K 138 SER cc_start: 0.8286 (t) cc_final: 0.7905 (p) REVERT: L 24 TYR cc_start: 0.8633 (t80) cc_final: 0.7791 (t80) REVERT: L 82 TYR cc_start: 0.8292 (m-80) cc_final: 0.7870 (m-80) REVERT: L 116 ASP cc_start: 0.8128 (t0) cc_final: 0.7784 (t0) REVERT: L 118 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: L 138 SER cc_start: 0.8821 (t) cc_final: 0.8431 (p) REVERT: M 34 PHE cc_start: 0.8292 (t80) cc_final: 0.7978 (t80) REVERT: M 45 LYS cc_start: 0.8386 (mttt) cc_final: 0.8167 (mmmm) REVERT: M 101 PRO cc_start: 0.8058 (Cg_endo) cc_final: 0.7645 (Cg_exo) REVERT: M 107 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7483 (pp20) REVERT: N 86 ASN cc_start: 0.7449 (m-40) cc_final: 0.6652 (p0) REVERT: B 124 MET cc_start: 0.8726 (ttp) cc_final: 0.7243 (tmm) REVERT: C 262 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7797 (mp0) REVERT: A 16 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8353 (t0) REVERT: A 124 MET cc_start: 0.8947 (ttp) cc_final: 0.8414 (ttt) REVERT: H 49 ASP cc_start: 0.4372 (m-30) cc_final: 0.3036 (p0) REVERT: H 68 MET cc_start: 0.5275 (mmm) cc_final: 0.4047 (mmm) REVERT: H 173 PHE cc_start: 0.6658 (p90) cc_final: 0.6032 (p90) REVERT: H 239 PHE cc_start: 0.4473 (m-80) cc_final: 0.4108 (m-80) REVERT: F 13 GLU cc_start: 0.6523 (pm20) cc_final: 0.6035 (pm20) REVERT: F 57 TYR cc_start: 0.8554 (t80) cc_final: 0.8345 (t80) REVERT: F 115 ASP cc_start: 0.7434 (t0) cc_final: 0.6977 (t0) REVERT: F 184 TYR cc_start: 0.8459 (m-80) cc_final: 0.7669 (m-80) REVERT: F 248 MET cc_start: 0.8865 (mmm) cc_final: 0.8626 (mmm) REVERT: G 227 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.8370 (t80) outliers start: 81 outliers final: 64 residues processed: 437 average time/residue: 0.2430 time to fit residues: 166.1420 Evaluate side-chains 445 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 376 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain I residue 20 VAL 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 112 MET 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 59 ASP Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain L residue 113 ILE 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 56 MET Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 81 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 N residue 14 ILE 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 132 ASN Chi-restraints excluded: chain B residue 62 VAL 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 250 LEU Chi-restraints excluded: chain C residue 1 MET 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 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 D residue 11 ASN 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 229 LEU Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain H residue 37 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 34 LEU 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 201 PHE 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: 4.9990 chunk 264 optimal weight: 5.9990 chunk 216 optimal weight: 30.0000 chunk 222 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 253 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 300 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 104 GLN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 GLN C 16 ASN C 154 GLN A 16 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.104987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.077714 restraints weight = 140102.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.080332 restraints weight = 53353.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.081934 restraints weight = 30450.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.082863 restraints weight = 21949.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.083329 restraints weight = 18262.826| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25766 Z= 0.232 Angle : 0.612 28.247 34967 Z= 0.319 Chirality : 0.057 1.474 4072 Planarity : 0.004 0.055 4279 Dihedral : 10.874 156.063 4065 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.38 % Allowed : 13.68 % Favored : 81.93 % 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: 1.06 (0.15), residues: 3062 helix: 2.25 (0.14), residues: 1263 sheet: 0.90 (0.20), residues: 609 loop : -1.17 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 33 TYR 0.022 0.002 TYR B 125 PHE 0.017 0.002 PHE N 109 TRP 0.008 0.001 TRP H 138 HIS 0.006 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (25764) covalent geometry : angle 0.61221 / 0.32 (34967) hydrogen bonds : bond 0.04184 / 2.79 ( 1071) hydrogen bonds : angle 4.11236 / 2.94 ( 3102) Misc. bond : bond 0.00558 / 0.27 ( 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 483 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 368 time to evaluate : 1.124 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: J 128 MET cc_start: 0.8132 (ttt) cc_final: 0.7774 (ttt) REVERT: J 135 LYS cc_start: 0.7092 (mttt) cc_final: 0.6873 (mmtt) REVERT: I 16 ASN cc_start: 0.8468 (m-40) cc_final: 0.8188 (m110) REVERT: I 33 ARG cc_start: 0.8403 (mtm180) cc_final: 0.8143 (mtt90) REVERT: I 49 ASP cc_start: 0.9317 (m-30) cc_final: 0.8981 (m-30) REVERT: I 111 ARG cc_start: 0.8771 (ttm110) cc_final: 0.8406 (mtm-85) REVERT: I 121 ARG cc_start: 0.8868 (mtm-85) cc_final: 0.7860 (mtp-110) REVERT: I 132 ASN cc_start: 0.9264 (m-40) cc_final: 0.8777 (m110) REVERT: K 18 LEU cc_start: 0.9423 (mm) cc_final: 0.9172 (mm) REVERT: K 36 ASN cc_start: 0.8852 (t0) cc_final: 0.8626 (m110) REVERT: K 49 ASP cc_start: 0.9091 (m-30) cc_final: 0.8840 (m-30) REVERT: K 122 LYS cc_start: 0.8808 (tttt) cc_final: 0.8586 (mtmt) REVERT: K 126 LEU cc_start: 0.9512 (mm) cc_final: 0.9283 (mt) REVERT: K 128 MET cc_start: 0.8674 (tpp) cc_final: 0.8459 (tpp) REVERT: K 132 ASN cc_start: 0.8862 (m-40) cc_final: 0.8578 (m-40) REVERT: K 138 SER cc_start: 0.8400 (t) cc_final: 0.7970 (p) REVERT: L 24 TYR cc_start: 0.8709 (t80) cc_final: 0.7842 (t80) REVERT: L 116 ASP cc_start: 0.8097 (t0) cc_final: 0.7619 (t0) REVERT: L 118 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7073 (m-80) REVERT: L 138 SER cc_start: 0.8677 (t) cc_final: 0.8313 (p) REVERT: L 139 LYS cc_start: 0.8423 (pptt) cc_final: 0.8077 (pttt) REVERT: M 45 LYS cc_start: 0.8513 (mttt) cc_final: 0.8228 (mmmm) REVERT: M 59 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8218 (p0) REVERT: N 86 ASN cc_start: 0.7360 (m-40) cc_final: 0.6642 (p0) REVERT: N 138 SER cc_start: 0.5935 (t) cc_final: 0.5387 (p) REVERT: B 124 MET cc_start: 0.8902 (ttp) cc_final: 0.7552 (tmm) REVERT: C 262 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7836 (mp0) REVERT: C 275 MET cc_start: 0.8091 (tmm) cc_final: 0.7811 (tmm) REVERT: D 116 VAL cc_start: 0.9296 (m) cc_final: 0.9051 (p) REVERT: A 16 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8233 (t0) REVERT: A 124 MET cc_start: 0.8946 (ttp) cc_final: 0.8454 (ttt) REVERT: H 68 MET cc_start: 0.5275 (mmm) cc_final: 0.3763 (mmm) REVERT: H 173 PHE cc_start: 0.6407 (p90) cc_final: 0.5649 (p90) REVERT: E 245 MET cc_start: 0.8490 (mmm) cc_final: 0.8156 (mmm) REVERT: F 115 ASP cc_start: 0.7469 (t0) cc_final: 0.7077 (t0) REVERT: F 154 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7241 (tm-30) REVERT: F 160 HIS cc_start: 0.8175 (m-70) cc_final: 0.7908 (m-70) REVERT: F 184 TYR cc_start: 0.8561 (m-80) cc_final: 0.7825 (m-80) REVERT: G 227 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8378 (t80) REVERT: G 296 ASN cc_start: 0.7570 (m-40) cc_final: 0.6792 (t0) outliers start: 115 outliers final: 88 residues processed: 428 average time/residue: 0.2420 time to fit residues: 162.5563 Evaluate side-chains 443 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 351 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 117 VAL 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 47 LEU Chi-restraints excluded: chain I residue 55 GLN 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 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 96 VAL Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain L residue 39 SER 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 122 LYS Chi-restraints excluded: chain M residue 14 ILE 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 59 ASP Chi-restraints excluded: chain M residue 81 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 M residue 134 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 49 ASP Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 129 SER 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 154 GLN 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 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 161 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 245 MET 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 62 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 229 LEU 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 16 ASN Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 161 VAL 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 82 ASP 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 F residue 266 ASP Chi-restraints excluded: chain G residue 137 ILE 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 Chi-restraints excluded: chain G residue 314 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 153 optimal weight: 0.4980 chunk 239 optimal weight: 4.9990 chunk 289 optimal weight: 6.9990 chunk 113 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** C 16 ASN A 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.104918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.077714 restraints weight = 139421.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.080334 restraints weight = 52902.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.081937 restraints weight = 30202.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.082857 restraints weight = 21739.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.083341 restraints weight = 18094.018| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25766 Z= 0.147 Angle : 0.531 33.004 34967 Z= 0.276 Chirality : 0.055 1.462 4072 Planarity : 0.003 0.044 4279 Dihedral : 10.787 151.522 4065 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.21 % Allowed : 15.61 % Favored : 81.18 % 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: 1.25 (0.15), residues: 3062 helix: 2.45 (0.14), residues: 1263 sheet: 0.92 (0.20), residues: 597 loop : -1.06 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 133 TYR 0.019 0.001 TYR L 48 PHE 0.014 0.001 PHE N 109 TRP 0.017 0.002 TRP H 12 HIS 0.005 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (25764) covalent geometry : angle 0.53051 / 0.28 (34967) hydrogen bonds : bond 0.03632 / 2.43 ( 1071) hydrogen bonds : angle 3.81294 / 2.72 ( 3102) Misc. bond : bond 0.00123 / 0.06 ( 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 446 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 362 time to evaluate : 1.143 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: I 16 ASN cc_start: 0.8490 (m-40) cc_final: 0.8236 (m110) REVERT: I 49 ASP cc_start: 0.9249 (m-30) cc_final: 0.8945 (m-30) REVERT: I 111 ARG cc_start: 0.8823 (ttm110) cc_final: 0.8497 (mtm-85) REVERT: I 132 ASN cc_start: 0.9230 (m-40) cc_final: 0.8736 (m110) REVERT: K 18 LEU cc_start: 0.9355 (mm) cc_final: 0.9100 (mm) REVERT: K 49 ASP cc_start: 0.9091 (m-30) cc_final: 0.8837 (m-30) REVERT: K 122 LYS cc_start: 0.8832 (tttt) cc_final: 0.8465 (mtmt) REVERT: K 126 LEU cc_start: 0.9489 (mm) cc_final: 0.9264 (mt) REVERT: K 128 MET cc_start: 0.8661 (tpp) cc_final: 0.8420 (tpp) REVERT: K 132 ASN cc_start: 0.8856 (m-40) cc_final: 0.8501 (m110) REVERT: K 138 SER cc_start: 0.8364 (t) cc_final: 0.7946 (p) REVERT: L 24 TYR cc_start: 0.8679 (t80) cc_final: 0.7970 (t80) REVERT: L 116 ASP cc_start: 0.8290 (t0) cc_final: 0.7859 (t0) REVERT: L 118 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: L 138 SER cc_start: 0.8678 (t) cc_final: 0.8310 (p) REVERT: L 139 LYS cc_start: 0.8257 (pptt) cc_final: 0.7870 (pttt) REVERT: M 45 LYS cc_start: 0.8496 (mttt) cc_final: 0.8249 (mmmm) REVERT: M 59 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8139 (p0) REVERT: M 107 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7381 (pp20) REVERT: N 33 ARG cc_start: 0.8481 (tpm170) cc_final: 0.8248 (tpm170) REVERT: N 49 ASP cc_start: 0.8460 (m-30) cc_final: 0.7975 (p0) REVERT: N 86 ASN cc_start: 0.7346 (m-40) cc_final: 0.6666 (p0) REVERT: N 94 TYR cc_start: 0.5805 (m-80) cc_final: 0.5356 (m-80) REVERT: B 124 MET cc_start: 0.8881 (ttp) cc_final: 0.7463 (tmm) REVERT: C 262 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7832 (mp0) REVERT: D 1 MET cc_start: 0.8006 (mtp) cc_final: 0.7779 (ttp) REVERT: D 116 VAL cc_start: 0.9219 (m) cc_final: 0.9001 (p) REVERT: D 267 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8082 (t0) REVERT: A 124 MET cc_start: 0.8827 (ttp) cc_final: 0.8137 (ttt) REVERT: H 68 MET cc_start: 0.5449 (mmm) cc_final: 0.3968 (mmm) REVERT: H 173 PHE cc_start: 0.6341 (p90) cc_final: 0.5641 (p90) REVERT: E 245 MET cc_start: 0.8601 (mmm) cc_final: 0.8242 (mmm) REVERT: F 115 ASP cc_start: 0.7136 (t0) cc_final: 0.6644 (t0) REVERT: F 154 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7253 (tm-30) REVERT: F 184 TYR cc_start: 0.8555 (m-80) cc_final: 0.7801 (m-80) REVERT: G 124 MET cc_start: 0.7047 (ttt) cc_final: 0.6747 (ttt) REVERT: G 227 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8351 (t80) REVERT: G 296 ASN cc_start: 0.7584 (m-40) cc_final: 0.6816 (t0) outliers start: 84 outliers final: 62 residues processed: 409 average time/residue: 0.2408 time to fit residues: 154.8604 Evaluate side-chains 414 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 347 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 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 136 LEU 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 136 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 82 TYR Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 118 TYR Chi-restraints excluded: chain L residue 122 LYS 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 39 SER Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 65 THR 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 N residue 14 ILE Chi-restraints excluded: chain N residue 20 VAL 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 132 ASN Chi-restraints excluded: chain B residue 154 GLN 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 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 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 13 GLU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 161 VAL 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 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 F residue 266 ASP Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 227 TYR Chi-restraints excluded: chain G residue 285 ASN 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: 0.0570 chunk 179 optimal weight: 0.7980 chunk 291 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 30.0000 chunk 10 optimal weight: 7.9990 chunk 285 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 270 optimal weight: 0.7980 overall best weight: 2.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** C 16 ASN A 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.104073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.076747 restraints weight = 146913.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.079386 restraints weight = 54883.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.081004 restraints weight = 30993.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.081924 restraints weight = 22167.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.082472 restraints weight = 18434.764| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25766 Z= 0.158 Angle : 0.552 36.180 34967 Z= 0.283 Chirality : 0.055 1.462 4072 Planarity : 0.003 0.043 4279 Dihedral : 10.744 147.513 4065 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.59 % Allowed : 15.27 % Favored : 81.14 % 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: 1.24 (0.15), residues: 3062 helix: 2.46 (0.14), residues: 1263 sheet: 0.84 (0.21), residues: 600 loop : -1.05 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 133 TYR 0.015 0.001 TYR B 125 PHE 0.033 0.001 PHE N 109 TRP 0.004 0.001 TRP H 138 HIS 0.004 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (25764) covalent geometry : angle 0.55161 / 0.28 (34967) hydrogen bonds : bond 0.03598 / 2.41 ( 1071) hydrogen bonds : angle 3.81204 / 2.72 ( 3102) Misc. bond : bond 0.00235 / 0.11 ( 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 444 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 350 time to evaluate : 1.189 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 135 LYS cc_start: 0.6511 (mttt) cc_final: 0.5998 (mmtt) REVERT: I 16 ASN cc_start: 0.8689 (m-40) cc_final: 0.8416 (m110) REVERT: I 49 ASP cc_start: 0.9282 (m-30) cc_final: 0.8947 (m-30) REVERT: I 55 GLN cc_start: 0.9253 (tm-30) cc_final: 0.8708 (pp30) REVERT: I 121 ARG cc_start: 0.8913 (mtm-85) cc_final: 0.7976 (mtp-110) REVERT: I 132 ASN cc_start: 0.9261 (m-40) cc_final: 0.8725 (m110) REVERT: I 139 LYS cc_start: 0.8620 (tppt) cc_final: 0.8190 (mmtm) REVERT: I 140 GLN cc_start: 0.7777 (pt0) cc_final: 0.7546 (pt0) REVERT: K 18 LEU cc_start: 0.9380 (mm) cc_final: 0.9146 (mm) REVERT: K 49 ASP cc_start: 0.9094 (m-30) cc_final: 0.8854 (m-30) REVERT: K 122 LYS cc_start: 0.8842 (tttt) cc_final: 0.8534 (mtmt) REVERT: K 126 LEU cc_start: 0.9552 (mm) cc_final: 0.9308 (mt) REVERT: K 132 ASN cc_start: 0.8889 (m-40) cc_final: 0.8461 (m110) REVERT: K 138 SER cc_start: 0.8382 (t) cc_final: 0.7964 (p) REVERT: L 24 TYR cc_start: 0.8695 (t80) cc_final: 0.7982 (t80) REVERT: L 41 GLU cc_start: 0.8419 (mp0) cc_final: 0.8103 (mp0) REVERT: L 116 ASP cc_start: 0.8293 (t0) cc_final: 0.7898 (t0) REVERT: L 118 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: L 138 SER cc_start: 0.8640 (t) cc_final: 0.8284 (p) REVERT: L 139 LYS cc_start: 0.8112 (pptt) cc_final: 0.7583 (pttt) REVERT: M 45 LYS cc_start: 0.8517 (mttt) cc_final: 0.8252 (mmmm) REVERT: M 59 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8016 (p0) REVERT: N 22 PHE cc_start: 0.8900 (t80) cc_final: 0.8336 (t80) REVERT: N 49 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.7993 (p0) REVERT: N 86 ASN cc_start: 0.7417 (m-40) cc_final: 0.6702 (p0) REVERT: N 94 TYR cc_start: 0.5636 (m-80) cc_final: 0.5136 (m-80) REVERT: B 112 MET cc_start: 0.7973 (ttm) cc_final: 0.7537 (mtt) REVERT: B 124 MET cc_start: 0.8903 (ttp) cc_final: 0.7472 (tmm) REVERT: C 262 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7848 (mp0) REVERT: C 275 MET cc_start: 0.8255 (tmm) cc_final: 0.8023 (tmm) REVERT: D 1 MET cc_start: 0.8011 (mtp) cc_final: 0.7793 (ttp) REVERT: D 267 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8143 (t0) REVERT: A 124 MET cc_start: 0.8779 (ttp) cc_final: 0.8118 (ttt) REVERT: H 68 MET cc_start: 0.5863 (mmm) cc_final: 0.4263 (mmm) REVERT: H 173 PHE cc_start: 0.6575 (p90) cc_final: 0.5620 (p90) REVERT: E 245 MET cc_start: 0.8547 (mmm) cc_final: 0.8173 (mmm) REVERT: F 115 ASP cc_start: 0.7087 (t0) cc_final: 0.6656 (t0) REVERT: F 154 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7323 (tm-30) REVERT: F 184 TYR cc_start: 0.8711 (m-80) cc_final: 0.8078 (m-80) REVERT: G 227 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8376 (t80) REVERT: G 296 ASN cc_start: 0.7596 (m-40) cc_final: 0.6831 (t0) outliers start: 94 outliers final: 77 residues processed: 407 average time/residue: 0.2351 time to fit residues: 151.8148 Evaluate side-chains 419 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 337 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 117 VAL 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 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 31 VAL Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 119 TYR Chi-restraints excluded: chain K residue 136 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 122 LYS Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain M residue 10 ILE 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 47 LEU Chi-restraints excluded: chain M residue 59 ASP 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 14 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 49 ASP Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 132 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 250 LEU 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 223 ILE Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain A residue 16 ASN 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 H residue 111 LYS 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 F residue 266 ASP Chi-restraints excluded: chain G residue 137 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 263 optimal weight: 7.9990 chunk 229 optimal weight: 0.5980 chunk 46 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 chunk 287 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 291 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 88 ASN A 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.102803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075266 restraints weight = 144973.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.077831 restraints weight = 54955.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.079404 restraints weight = 31632.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.080315 restraints weight = 23003.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.080768 restraints weight = 19234.555| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25766 Z= 0.229 Angle : 0.581 17.711 34967 Z= 0.308 Chirality : 0.056 1.484 4072 Planarity : 0.004 0.070 4279 Dihedral : 10.828 143.772 4065 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 26.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.78 % Allowed : 15.95 % Favored : 80.27 % 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: 0.95 (0.15), residues: 3062 helix: 2.26 (0.14), residues: 1263 sheet: 0.50 (0.21), residues: 611 loop : -1.13 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 111 TYR 0.017 0.001 TYR M 118 PHE 0.013 0.001 PHE H 173 TRP 0.005 0.001 TRP H 12 HIS 0.005 0.001 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.23 (25764) covalent geometry : angle 0.58098 / 0.31 (34967) hydrogen bonds : bond 0.03841 / 2.57 ( 1071) hydrogen bonds : angle 4.02610 / 2.89 ( 3102) Misc. bond : bond 0.00094 / 0.05 ( 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 438 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 339 time to evaluate : 1.242 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 133 ARG cc_start: 0.8221 (mtp-110) cc_final: 0.7888 (mtp-110) REVERT: I 16 ASN cc_start: 0.8700 (m-40) cc_final: 0.8427 (m110) REVERT: I 33 ARG cc_start: 0.8493 (mtm180) cc_final: 0.8167 (mtm180) REVERT: I 49 ASP cc_start: 0.9271 (m-30) cc_final: 0.8937 (m-30) REVERT: I 121 ARG cc_start: 0.8933 (mtm-85) cc_final: 0.7982 (mtp-110) REVERT: I 132 ASN cc_start: 0.9207 (m-40) cc_final: 0.8867 (m110) REVERT: I 136 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7703 (pp) REVERT: I 140 GLN cc_start: 0.7798 (pt0) cc_final: 0.7527 (pt0) REVERT: K 18 LEU cc_start: 0.9413 (mm) cc_final: 0.9178 (mm) REVERT: K 49 ASP cc_start: 0.9128 (m-30) cc_final: 0.8902 (m-30) REVERT: K 122 LYS cc_start: 0.8780 (tttt) cc_final: 0.8444 (mtmm) REVERT: K 126 LEU cc_start: 0.9563 (mm) cc_final: 0.9312 (mt) REVERT: K 132 ASN cc_start: 0.8920 (m-40) cc_final: 0.8458 (m110) REVERT: K 138 SER cc_start: 0.8411 (t) cc_final: 0.7995 (p) REVERT: L 116 ASP cc_start: 0.8356 (t0) cc_final: 0.7957 (t0) REVERT: L 118 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: L 138 SER cc_start: 0.8674 (t) cc_final: 0.8317 (p) REVERT: L 139 LYS cc_start: 0.8173 (pptt) cc_final: 0.7631 (pttt) REVERT: M 45 LYS cc_start: 0.8534 (mttt) cc_final: 0.8243 (mmmm) REVERT: M 59 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8025 (p0) REVERT: M 99 TYR cc_start: 0.7711 (m-80) cc_final: 0.7467 (m-80) REVERT: N 33 ARG cc_start: 0.8461 (tpm170) cc_final: 0.8200 (tpm170) REVERT: N 86 ASN cc_start: 0.7446 (m-40) cc_final: 0.6748 (p0) REVERT: B 112 MET cc_start: 0.7987 (ttm) cc_final: 0.7564 (mtt) REVERT: B 124 MET cc_start: 0.8943 (ttp) cc_final: 0.7585 (tmm) REVERT: C 262 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7863 (mp0) REVERT: C 275 MET cc_start: 0.8266 (tmm) cc_final: 0.8031 (tmm) REVERT: D 267 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8167 (t0) REVERT: A 124 MET cc_start: 0.8693 (ttp) cc_final: 0.7850 (ttt) REVERT: H 68 MET cc_start: 0.5865 (mmm) cc_final: 0.4256 (mmm) REVERT: H 173 PHE cc_start: 0.6723 (p90) cc_final: 0.5566 (p90) REVERT: F 124 MET cc_start: 0.8313 (ttt) cc_final: 0.7766 (ttp) REVERT: F 154 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7361 (tm-30) REVERT: F 184 TYR cc_start: 0.8726 (m-80) cc_final: 0.8186 (m-80) REVERT: G 227 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8417 (t80) REVERT: G 296 ASN cc_start: 0.7678 (m-40) cc_final: 0.6916 (t0) outliers start: 99 outliers final: 87 residues processed: 397 average time/residue: 0.2088 time to fit residues: 131.8678 Evaluate side-chains 419 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 327 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 117 VAL 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 117 VAL Chi-restraints excluded: chain I residue 136 LEU 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 31 VAL 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 31 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 82 TYR Chi-restraints excluded: chain L residue 96 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 122 LYS Chi-restraints excluded: chain L residue 134 ILE 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 39 SER Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 32 ASP 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 132 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 250 LEU 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 223 ILE Chi-restraints excluded: chain C residue 245 MET 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 197 VAL Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 LEU 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 82 ASP 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 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 Chi-restraints excluded: chain G residue 285 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 90 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 276 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** A 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.102930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.075142 restraints weight = 158248.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.077828 restraints weight = 57536.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.079449 restraints weight = 32533.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.080416 restraints weight = 23397.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.080939 restraints weight = 19414.256| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25766 Z= 0.160 Angle : 0.516 17.874 34967 Z= 0.278 Chirality : 0.055 1.474 4072 Planarity : 0.003 0.043 4279 Dihedral : 10.744 140.407 4065 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 25.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.48 % Allowed : 16.55 % Favored : 79.97 % 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: 1.07 (0.15), residues: 3062 helix: 2.43 (0.14), residues: 1258 sheet: 0.55 (0.21), residues: 596 loop : -1.13 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 111 TYR 0.014 0.001 TYR L 48 PHE 0.012 0.001 PHE E 159 TRP 0.006 0.001 TRP H 12 HIS 0.004 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (25764) covalent geometry : angle 0.51610 / 0.28 (34967) hydrogen bonds : bond 0.03546 / 2.37 ( 1071) hydrogen bonds : angle 3.83178 / 2.75 ( 3102) Misc. bond : bond 0.00026 / 0.01 ( 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 429 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 338 time to evaluate : 1.255 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: 0.8300 (mtp-110) cc_final: 0.8027 (mtp-110) REVERT: J 135 LYS cc_start: 0.6486 (mttt) cc_final: 0.5977 (mmtt) REVERT: I 16 ASN cc_start: 0.8700 (m-40) cc_final: 0.8442 (m110) REVERT: I 29 THR cc_start: 0.8723 (m) cc_final: 0.8483 (m) REVERT: I 30 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8577 (pp) REVERT: I 49 ASP cc_start: 0.9250 (m-30) cc_final: 0.8926 (m-30) REVERT: I 121 ARG cc_start: 0.8931 (mtm-85) cc_final: 0.8535 (mtm-85) REVERT: I 132 ASN cc_start: 0.9203 (m-40) cc_final: 0.8767 (m110) REVERT: I 139 LYS cc_start: 0.8581 (tppt) cc_final: 0.8165 (mmtm) REVERT: I 140 GLN cc_start: 0.7862 (pt0) cc_final: 0.7523 (pt0) REVERT: K 18 LEU cc_start: 0.9402 (mm) cc_final: 0.9149 (mm) REVERT: K 49 ASP cc_start: 0.9087 (m-30) cc_final: 0.8883 (m-30) REVERT: K 122 LYS cc_start: 0.8876 (tttt) cc_final: 0.8533 (mtmt) REVERT: K 126 LEU cc_start: 0.9549 (mm) cc_final: 0.9306 (mt) REVERT: K 132 ASN cc_start: 0.8909 (m-40) cc_final: 0.8399 (m110) REVERT: K 138 SER cc_start: 0.8402 (t) cc_final: 0.7989 (p) REVERT: L 116 ASP cc_start: 0.8349 (t0) cc_final: 0.7938 (t0) REVERT: L 118 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: L 138 SER cc_start: 0.8664 (t) cc_final: 0.8305 (p) REVERT: L 139 LYS cc_start: 0.8185 (pptt) cc_final: 0.7645 (pttt) REVERT: M 45 LYS cc_start: 0.8464 (mttt) cc_final: 0.8134 (mmmm) REVERT: M 59 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.7996 (p0) REVERT: M 99 TYR cc_start: 0.7805 (m-80) cc_final: 0.7492 (m-80) REVERT: M 122 LYS cc_start: 0.8862 (pttt) cc_final: 0.8654 (ptpp) REVERT: N 22 PHE cc_start: 0.8749 (t80) cc_final: 0.8250 (t80) REVERT: N 33 ARG cc_start: 0.8525 (tpm170) cc_final: 0.8299 (tpm170) REVERT: N 86 ASN cc_start: 0.7477 (m-40) cc_final: 0.6767 (p0) REVERT: B 112 MET cc_start: 0.7926 (ttm) cc_final: 0.7529 (mtt) REVERT: B 124 MET cc_start: 0.8925 (ttp) cc_final: 0.7595 (tmm) REVERT: C 275 MET cc_start: 0.8270 (tmm) cc_final: 0.8018 (tmm) REVERT: D 267 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8235 (t0) REVERT: A 16 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8064 (t0) REVERT: A 124 MET cc_start: 0.8626 (ttp) cc_final: 0.7882 (ttt) REVERT: H 68 MET cc_start: 0.5874 (mmm) cc_final: 0.4262 (mmm) REVERT: H 173 PHE cc_start: 0.6723 (p90) cc_final: 0.5501 (p90) REVERT: F 124 MET cc_start: 0.8240 (ttt) cc_final: 0.7701 (ttp) REVERT: F 154 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7306 (tm-30) REVERT: F 184 TYR cc_start: 0.8729 (m-80) cc_final: 0.8194 (m-80) REVERT: G 137 ILE cc_start: 0.9428 (pt) cc_final: 0.9046 (mt) REVERT: G 296 ASN cc_start: 0.7696 (m-40) cc_final: 0.6909 (t0) outliers start: 91 outliers final: 79 residues processed: 389 average time/residue: 0.2280 time to fit residues: 140.8959 Evaluate side-chains 410 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 326 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 117 VAL 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 96 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 31 VAL Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 43 VAL 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 L residue 122 LYS Chi-restraints excluded: chain L residue 134 ILE 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 47 LEU 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 117 VAL Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 20 VAL 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 129 SER Chi-restraints excluded: chain N residue 132 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 316 VAL 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 245 MET 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 305 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain A residue 16 ASN 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 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 201 PHE 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: 2.9990 chunk 234 optimal weight: 3.9990 chunk 167 optimal weight: 0.0370 chunk 100 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 179 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** C 16 ASN A 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.103279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.075998 restraints weight = 153104.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.078673 restraints weight = 56273.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.080299 restraints weight = 31595.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.081259 restraints weight = 22546.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.081759 restraints weight = 18623.726| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25766 Z= 0.109 Angle : 0.491 17.875 34967 Z= 0.263 Chirality : 0.055 1.452 4072 Planarity : 0.003 0.042 4279 Dihedral : 10.669 139.679 4065 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 25.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.91 % Allowed : 17.80 % Favored : 79.29 % 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: 1.25 (0.15), residues: 3062 helix: 2.61 (0.15), residues: 1258 sheet: 0.63 (0.21), residues: 598 loop : -1.06 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 60 TYR 0.017 0.001 TYR I 24 PHE 0.015 0.001 PHE N 109 TRP 0.010 0.001 TRP H 12 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (25764) covalent geometry : angle 0.49137 / 0.26 (34967) hydrogen bonds : bond 0.03352 / 2.24 ( 1071) hydrogen bonds : angle 3.65502 / 2.63 ( 3102) Misc. bond : bond 0.00033 / 0.02 ( 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 409 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 333 time to evaluate : 1.108 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: J 133 ARG cc_start: 0.8298 (mtp-110) cc_final: 0.8038 (mtp-110) REVERT: J 135 LYS cc_start: 0.6459 (mttt) cc_final: 0.5955 (mmtt) REVERT: I 16 ASN cc_start: 0.8713 (m-40) cc_final: 0.8465 (m110) REVERT: I 29 THR cc_start: 0.8845 (m) cc_final: 0.8614 (m) REVERT: I 30 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8498 (pp) REVERT: I 49 ASP cc_start: 0.9244 (m-30) cc_final: 0.8917 (m-30) REVERT: I 121 ARG cc_start: 0.8860 (mtm-85) cc_final: 0.8500 (mtm-85) REVERT: I 132 ASN cc_start: 0.9100 (m-40) cc_final: 0.8813 (m110) REVERT: I 139 LYS cc_start: 0.8543 (tppt) cc_final: 0.8148 (mmtm) REVERT: I 140 GLN cc_start: 0.7829 (pt0) cc_final: 0.7603 (pt0) REVERT: K 18 LEU cc_start: 0.9378 (mm) cc_final: 0.9147 (mm) REVERT: K 122 LYS cc_start: 0.8847 (tttt) cc_final: 0.8522 (mtmt) REVERT: K 126 LEU cc_start: 0.9541 (mm) cc_final: 0.9295 (mt) REVERT: K 132 ASN cc_start: 0.8908 (m-40) cc_final: 0.8387 (m110) REVERT: K 138 SER cc_start: 0.8390 (t) cc_final: 0.7978 (p) REVERT: L 116 ASP cc_start: 0.8325 (t0) cc_final: 0.7930 (t0) REVERT: L 118 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: L 138 SER cc_start: 0.8651 (t) cc_final: 0.8289 (p) REVERT: L 139 LYS cc_start: 0.8169 (pptt) cc_final: 0.7637 (pttt) REVERT: M 45 LYS cc_start: 0.8445 (mttt) cc_final: 0.8118 (mmmm) REVERT: M 59 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8066 (p0) REVERT: M 99 TYR cc_start: 0.7801 (m-80) cc_final: 0.7486 (m-80) REVERT: N 86 ASN cc_start: 0.7476 (m-40) cc_final: 0.6568 (p0) REVERT: B 112 MET cc_start: 0.7898 (ttm) cc_final: 0.7507 (mtt) REVERT: B 124 MET cc_start: 0.8922 (ttp) cc_final: 0.7550 (tmm) REVERT: C 97 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: D 267 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8240 (t0) REVERT: A 16 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.7994 (t0) REVERT: A 124 MET cc_start: 0.8649 (ttp) cc_final: 0.7933 (ttt) REVERT: H 68 MET cc_start: 0.5906 (mmm) cc_final: 0.4278 (mmm) REVERT: H 173 PHE cc_start: 0.6660 (p90) cc_final: 0.5444 (p90) REVERT: E 124 MET cc_start: 0.8103 (tmm) cc_final: 0.7893 (ptm) REVERT: F 124 MET cc_start: 0.8293 (ttt) cc_final: 0.7762 (ttp) REVERT: F 154 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7309 (tm-30) REVERT: F 184 TYR cc_start: 0.8712 (m-80) cc_final: 0.8453 (m-80) REVERT: G 124 MET cc_start: 0.7607 (ttp) cc_final: 0.7073 (ttp) REVERT: G 137 ILE cc_start: 0.9425 (pt) cc_final: 0.9045 (mt) REVERT: G 296 ASN cc_start: 0.7671 (m-40) cc_final: 0.6869 (t0) outliers start: 76 outliers final: 66 residues processed: 380 average time/residue: 0.2272 time to fit residues: 137.0974 Evaluate side-chains 399 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 327 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 10 ILE 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 117 VAL 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 86 ASN 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 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 113 ILE Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 118 TYR Chi-restraints excluded: chain L residue 122 LYS 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 59 ASP Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 20 VAL 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 132 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 ASN 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 97 GLU 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 245 MET 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 197 VAL Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain A residue 16 ASN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 7 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 154 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** A 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.103206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.075456 restraints weight = 161703.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.078178 restraints weight = 58222.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.079837 restraints weight = 32608.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.080821 restraints weight = 23330.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.081362 restraints weight = 19311.775| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25766 Z= 0.128 Angle : 0.506 17.843 34967 Z= 0.269 Chirality : 0.055 1.456 4072 Planarity : 0.003 0.042 4279 Dihedral : 10.655 139.270 4065 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.83 % Allowed : 18.07 % Favored : 79.10 % 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: 1.25 (0.15), residues: 3062 helix: 2.62 (0.15), residues: 1258 sheet: 0.61 (0.21), residues: 599 loop : -1.06 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 60 TYR 0.014 0.001 TYR I 24 PHE 0.010 0.001 PHE M 22 TRP 0.008 0.001 TRP H 12 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (25764) covalent geometry : angle 0.50621 / 0.27 (34967) hydrogen bonds : bond 0.03336 / 2.23 ( 1071) hydrogen bonds : angle 3.68526 / 2.65 ( 3102) Misc. bond : bond 0.00031 / 0.02 ( 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 403 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 329 time to evaluate : 0.867 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: 0.8387 (mtp-110) cc_final: 0.8147 (mtp-110) REVERT: J 135 LYS cc_start: 0.6446 (mttt) cc_final: 0.5924 (mmtt) REVERT: I 16 ASN cc_start: 0.8721 (m-40) cc_final: 0.8476 (m110) REVERT: I 29 THR cc_start: 0.8848 (m) cc_final: 0.8616 (m) REVERT: I 30 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8503 (pp) REVERT: I 49 ASP cc_start: 0.9241 (m-30) cc_final: 0.8931 (m-30) REVERT: I 121 ARG cc_start: 0.8891 (mtm-85) cc_final: 0.8054 (mtp-110) REVERT: I 132 ASN cc_start: 0.9127 (m-40) cc_final: 0.8823 (m110) REVERT: I 139 LYS cc_start: 0.8514 (tppt) cc_final: 0.8126 (mmtm) REVERT: I 140 GLN cc_start: 0.7878 (pt0) cc_final: 0.7626 (pt0) REVERT: K 18 LEU cc_start: 0.9373 (mm) cc_final: 0.9142 (mm) REVERT: K 122 LYS cc_start: 0.8856 (tttt) cc_final: 0.8523 (mtmt) REVERT: K 126 LEU cc_start: 0.9541 (mm) cc_final: 0.9295 (mt) REVERT: K 132 ASN cc_start: 0.8910 (m-40) cc_final: 0.8372 (m110) REVERT: K 138 SER cc_start: 0.8381 (t) cc_final: 0.7973 (p) REVERT: L 116 ASP cc_start: 0.8271 (t0) cc_final: 0.7910 (t0) REVERT: L 118 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: L 138 SER cc_start: 0.8640 (t) cc_final: 0.8301 (p) REVERT: L 139 LYS cc_start: 0.8179 (pptt) cc_final: 0.7647 (pttt) REVERT: M 45 LYS cc_start: 0.8441 (mttt) cc_final: 0.8112 (mmmm) REVERT: M 59 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8069 (p0) REVERT: M 99 TYR cc_start: 0.7815 (m-80) cc_final: 0.7494 (m-80) REVERT: N 22 PHE cc_start: 0.8923 (t80) cc_final: 0.8378 (t80) REVERT: N 86 ASN cc_start: 0.7783 (m-40) cc_final: 0.7000 (p0) REVERT: N 99 TYR cc_start: 0.4533 (OUTLIER) cc_final: 0.3955 (t80) REVERT: B 112 MET cc_start: 0.7957 (ttm) cc_final: 0.7573 (mtt) REVERT: B 124 MET cc_start: 0.8916 (ttp) cc_final: 0.7539 (tmm) REVERT: C 97 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: D 267 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8253 (t0) REVERT: A 124 MET cc_start: 0.8673 (ttp) cc_final: 0.7942 (ttt) REVERT: H 68 MET cc_start: 0.5898 (mmm) cc_final: 0.4270 (mmm) REVERT: H 173 PHE cc_start: 0.6700 (p90) cc_final: 0.5462 (p90) REVERT: F 154 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7316 (tm-30) REVERT: F 184 TYR cc_start: 0.8723 (m-80) cc_final: 0.8458 (m-80) REVERT: G 124 MET cc_start: 0.7559 (ttp) cc_final: 0.7004 (ttp) REVERT: G 137 ILE cc_start: 0.9430 (pt) cc_final: 0.9051 (mt) REVERT: G 296 ASN cc_start: 0.7686 (m-40) cc_final: 0.6880 (t0) outliers start: 74 outliers final: 68 residues processed: 372 average time/residue: 0.2364 time to fit residues: 139.1299 Evaluate side-chains 399 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 325 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 10 ILE 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 117 VAL 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 62 GLU Chi-restraints excluded: chain I residue 86 ASN 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 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 113 ILE Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 118 TYR Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 14 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 59 ASP Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 20 VAL 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 99 TYR Chi-restraints excluded: chain N residue 132 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 250 LEU 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 97 GLU 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 245 MET Chi-restraints excluded: chain C residue 252 VAL 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 197 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain A residue 16 ASN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 167 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 128 optimal weight: 0.0060 chunk 259 optimal weight: 5.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.102941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.075761 restraints weight = 149112.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.078384 restraints weight = 55632.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.079967 restraints weight = 31552.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.080927 restraints weight = 22675.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.081427 restraints weight = 18772.653| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- 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 = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25766 Z= 0.124 Angle : 0.505 17.867 34967 Z= 0.268 Chirality : 0.055 1.461 4072 Planarity : 0.003 0.042 4279 Dihedral : 10.633 138.565 4065 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 25.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.14 % Allowed : 17.88 % Favored : 78.99 % 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: 1.28 (0.15), residues: 3062 helix: 2.64 (0.14), residues: 1259 sheet: 0.63 (0.21), residues: 597 loop : -1.05 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 111 TYR 0.012 0.001 TYR B 125 PHE 0.017 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/Z covalent geometry : bond 0.00282 / 0.12 (25764) covalent geometry : angle 0.50463 / 0.27 (34967) hydrogen bonds : bond 0.03300 / 2.20 ( 1071) hydrogen bonds : angle 3.65231 / 2.62 ( 3102) Misc. bond : bond 0.00034 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7783.13 seconds wall clock time: 133 minutes 52.58 seconds (8032.58 seconds total)