Starting phenix.real_space_refine on Sun Jul 5 07:20:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d60_30586/07_2026/7d60_30586.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d60_30586/07_2026/7d60_30586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d60_30586/07_2026/7d60_30586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d60_30586/07_2026/7d60_30586.map" model { file = "/net/cci-nas-00/data/ceres_data/7d60_30586/07_2026/7d60_30586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d60_30586/07_2026/7d60_30586.cif" } resolution = 2.61 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 55 5.49 5 S 220 5.16 5 C 17303 2.51 5 N 4224 2.21 5 O 4862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 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: 26664 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K Time building chain proxies: 3.16, per 1000 atoms: 0.12 Number of scatterers: 26664 At special positions: 0 Unit cell: (155.1, 156.2, 105.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 220 16.00 P 55 15.00 O 4862 8.00 N 4224 7.00 C 17303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 127 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 149 " distance=2.04 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 127 " distance=2.04 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 127 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 127 " distance=2.04 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 127 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 127 " distance=2.04 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 127 " distance=2.04 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 127 " distance=2.04 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 127 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 158 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 158 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 158 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 158 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 158 " distance=2.03 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 158 " distance=2.03 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 158 " distance=2.03 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS F 142 " - pdb=" SG CYS F 149 " distance=2.04 Simple disulfide: pdb=" SG CYS G 142 " - pdb=" SG CYS G 149 " distance=2.03 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 149 " distance=2.04 Simple disulfide: pdb=" SG CYS I 142 " - pdb=" SG CYS I 149 " distance=2.03 Simple disulfide: pdb=" SG CYS J 142 " - pdb=" SG CYS J 149 " distance=2.04 Simple disulfide: pdb=" SG CYS K 142 " - pdb=" SG CYS K 149 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.0 seconds 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6006 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 0 sheets defined 79.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 9 through 14 removed outlier: 3.767A pdb=" N GLN A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.738A pdb=" N ILE A 18 " --> pdb=" O GLN A 14 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 69 removed outlier: 3.618A pdb=" N PHE A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Proline residue: A 58 - end of helix removed outlier: 3.562A pdb=" N PHE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 removed outlier: 3.958A pdb=" N TRP A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.613A pdb=" N VAL A 82 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 83 " --> pdb=" O CYS A 80 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.559A pdb=" N TYR A 98 " --> pdb=" O CYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 removed outlier: 3.875A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 131 removed outlier: 3.641A pdb=" N GLU A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY A 131 " --> pdb=" O CYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 removed outlier: 3.877A pdb=" N ILE A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.804A pdb=" N TRP A 150 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 3.598A pdb=" N LYS A 155 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 204 removed outlier: 3.778A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 247 removed outlier: 3.559A pdb=" N LYS A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 9 through 14 removed outlier: 3.766A pdb=" N GLN B 14 " --> pdb=" O PHE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 38 removed outlier: 3.738A pdb=" N ILE B 18 " --> pdb=" O GLN B 14 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 69 removed outlier: 3.617A pdb=" N PHE B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 55 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Proline residue: B 58 - end of helix removed outlier: 3.561A pdb=" N PHE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 78 removed outlier: 3.958A pdb=" N TRP B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 removed outlier: 3.613A pdb=" N VAL B 82 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 83 " --> pdb=" O CYS B 80 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 94 through 107 removed outlier: 3.558A pdb=" N TYR B 98 " --> pdb=" O CYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 removed outlier: 3.875A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 131 removed outlier: 3.641A pdb=" N GLU B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY B 131 " --> pdb=" O CYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 removed outlier: 3.877A pdb=" N ILE B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.804A pdb=" N TRP B 150 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 removed outlier: 3.598A pdb=" N LYS B 155 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 204 removed outlier: 3.778A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 247 removed outlier: 3.559A pdb=" N LYS B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 265 Processing helix chain 'B' and resid 279 through 288 Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 9 through 14 removed outlier: 3.767A pdb=" N GLN C 14 " --> pdb=" O PHE C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 38 removed outlier: 3.738A pdb=" N ILE C 18 " --> pdb=" O GLN C 14 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 69 removed outlier: 3.618A pdb=" N PHE C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Proline residue: C 58 - end of helix removed outlier: 3.561A pdb=" N PHE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 removed outlier: 3.957A pdb=" N TRP C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 removed outlier: 3.612A pdb=" N VAL C 82 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 83 " --> pdb=" O CYS C 80 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 94 through 107 removed outlier: 3.558A pdb=" N TYR C 98 " --> pdb=" O CYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.875A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 131 removed outlier: 3.642A pdb=" N GLU C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY C 131 " --> pdb=" O CYS C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 removed outlier: 3.876A pdb=" N ILE C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 removed outlier: 3.804A pdb=" N TRP C 150 " --> pdb=" O LYS C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.598A pdb=" N LYS C 155 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 204 removed outlier: 3.777A pdb=" N LEU C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 247 removed outlier: 3.560A pdb=" N LYS C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 224 " --> pdb=" O GLN C 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C 225 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 279 through 288 Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 9 through 14 removed outlier: 3.766A pdb=" N GLN D 14 " --> pdb=" O PHE D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 38 removed outlier: 3.738A pdb=" N ILE D 18 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 69 removed outlier: 3.618A pdb=" N PHE D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Proline residue: D 58 - end of helix removed outlier: 3.561A pdb=" N PHE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.957A pdb=" N TRP D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 3.612A pdb=" N VAL D 82 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN D 83 " --> pdb=" O CYS D 80 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 107 removed outlier: 3.558A pdb=" N TYR D 98 " --> pdb=" O CYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 removed outlier: 3.875A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 131 removed outlier: 3.641A pdb=" N GLU D 126 " --> pdb=" O GLY D 122 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY D 131 " --> pdb=" O CYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 142 removed outlier: 3.876A pdb=" N ILE D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.804A pdb=" N TRP D 150 " --> pdb=" O LYS D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 156 removed outlier: 3.599A pdb=" N LYS D 155 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 204 removed outlier: 3.778A pdb=" N LEU D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 247 removed outlier: 3.560A pdb=" N LYS D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 265 Processing helix chain 'D' and resid 279 through 288 Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 9 through 14 removed outlier: 3.766A pdb=" N GLN E 14 " --> pdb=" O PHE E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 38 removed outlier: 3.738A pdb=" N ILE E 18 " --> pdb=" O GLN E 14 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR E 20 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 69 removed outlier: 3.618A pdb=" N PHE E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Proline residue: E 58 - end of helix removed outlier: 3.562A pdb=" N PHE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 removed outlier: 3.958A pdb=" N TRP E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 87 removed outlier: 3.612A pdb=" N VAL E 82 " --> pdb=" O GLY E 79 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN E 83 " --> pdb=" O CYS E 80 " (cutoff:3.500A) Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 94 through 107 removed outlier: 3.558A pdb=" N TYR E 98 " --> pdb=" O CYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 121 removed outlier: 3.875A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 117 " --> pdb=" O MET E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 131 removed outlier: 3.641A pdb=" N GLU E 126 " --> pdb=" O GLY E 122 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY E 131 " --> pdb=" O CYS E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 removed outlier: 3.877A pdb=" N ILE E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.804A pdb=" N TRP E 150 " --> pdb=" O LYS E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 removed outlier: 3.598A pdb=" N LYS E 155 " --> pdb=" O GLU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 204 removed outlier: 3.778A pdb=" N LEU E 173 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 175 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN E 176 " --> pdb=" O LYS E 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN E 180 " --> pdb=" O GLN E 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 187 " --> pdb=" O GLY E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 247 removed outlier: 3.560A pdb=" N LYS E 221 " --> pdb=" O THR E 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E 225 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS E 236 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E 245 " --> pdb=" O ASN E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 265 Processing helix chain 'E' and resid 279 through 288 Processing helix chain 'F' and resid 2 through 8 Processing helix chain 'F' and resid 9 through 14 removed outlier: 3.766A pdb=" N GLN F 14 " --> pdb=" O PHE F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 38 removed outlier: 3.738A pdb=" N ILE F 18 " --> pdb=" O GLN F 14 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR F 20 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA F 24 " --> pdb=" O TYR F 20 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 36 " --> pdb=" O ARG F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 69 removed outlier: 3.618A pdb=" N PHE F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 55 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Proline residue: F 58 - end of helix removed outlier: 3.561A pdb=" N PHE F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 69 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 78 removed outlier: 3.957A pdb=" N TRP F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU F 76 " --> pdb=" O ARG F 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 87 removed outlier: 3.612A pdb=" N VAL F 82 " --> pdb=" O GLY F 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN F 83 " --> pdb=" O CYS F 80 " (cutoff:3.500A) Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 94 through 107 removed outlier: 3.558A pdb=" N TYR F 98 " --> pdb=" O CYS F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 121 removed outlier: 3.875A pdb=" N VAL F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 131 removed outlier: 3.641A pdb=" N GLU F 126 " --> pdb=" O GLY F 122 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY F 131 " --> pdb=" O CYS F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 removed outlier: 3.877A pdb=" N ILE F 141 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 removed outlier: 3.804A pdb=" N TRP F 150 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 156 removed outlier: 3.599A pdb=" N LYS F 155 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 204 removed outlier: 3.778A pdb=" N LEU F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER F 174 " --> pdb=" O GLU F 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 175 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN F 176 " --> pdb=" O LYS F 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN F 180 " --> pdb=" O GLN F 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU F 182 " --> pdb=" O GLN F 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 187 " --> pdb=" O GLY F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 247 removed outlier: 3.560A pdb=" N LYS F 221 " --> pdb=" O THR F 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU F 224 " --> pdb=" O GLN F 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN F 225 " --> pdb=" O LYS F 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE F 245 " --> pdb=" O ASN F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 265 Processing helix chain 'F' and resid 279 through 288 Processing helix chain 'G' and resid 2 through 8 Processing helix chain 'G' and resid 9 through 14 removed outlier: 3.767A pdb=" N GLN G 14 " --> pdb=" O PHE G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 38 removed outlier: 3.738A pdb=" N ILE G 18 " --> pdb=" O GLN G 14 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA G 24 " --> pdb=" O TYR G 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 69 removed outlier: 3.618A pdb=" N PHE G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G 55 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) Proline residue: G 58 - end of helix removed outlier: 3.561A pdb=" N PHE G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 78 removed outlier: 3.958A pdb=" N TRP G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU G 76 " --> pdb=" O ARG G 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 87 removed outlier: 3.613A pdb=" N VAL G 82 " --> pdb=" O GLY G 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN G 83 " --> pdb=" O CYS G 80 " (cutoff:3.500A) Proline residue: G 84 - end of helix Processing helix chain 'G' and resid 94 through 107 removed outlier: 3.558A pdb=" N TYR G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 121 removed outlier: 3.875A pdb=" N VAL G 112 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL G 117 " --> pdb=" O MET G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 131 removed outlier: 3.641A pdb=" N GLU G 126 " --> pdb=" O GLY G 122 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY G 131 " --> pdb=" O CYS G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 142 removed outlier: 3.877A pdb=" N ILE G 141 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 150 removed outlier: 3.804A pdb=" N TRP G 150 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 156 removed outlier: 3.598A pdb=" N LYS G 155 " --> pdb=" O GLU G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 204 removed outlier: 3.778A pdb=" N LEU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER G 174 " --> pdb=" O GLU G 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN G 176 " --> pdb=" O LYS G 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN G 178 " --> pdb=" O SER G 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN G 180 " --> pdb=" O GLN G 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 182 " --> pdb=" O GLN G 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 187 " --> pdb=" O GLY G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 247 removed outlier: 3.559A pdb=" N LYS G 221 " --> pdb=" O THR G 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU G 224 " --> pdb=" O GLN G 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN G 225 " --> pdb=" O LYS G 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE G 245 " --> pdb=" O ASN G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 265 Processing helix chain 'G' and resid 279 through 288 Processing helix chain 'H' and resid 2 through 8 Processing helix chain 'H' and resid 9 through 14 removed outlier: 3.767A pdb=" N GLN H 14 " --> pdb=" O PHE H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 38 removed outlier: 3.738A pdb=" N ILE H 18 " --> pdb=" O GLN H 14 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU H 33 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 69 removed outlier: 3.618A pdb=" N PHE H 54 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 55 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Proline residue: H 58 - end of helix removed outlier: 3.561A pdb=" N PHE H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 69 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 78 removed outlier: 3.958A pdb=" N TRP H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 87 removed outlier: 3.613A pdb=" N VAL H 82 " --> pdb=" O GLY H 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN H 83 " --> pdb=" O CYS H 80 " (cutoff:3.500A) Proline residue: H 84 - end of helix Processing helix chain 'H' and resid 94 through 107 removed outlier: 3.558A pdb=" N TYR H 98 " --> pdb=" O CYS H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 121 removed outlier: 3.875A pdb=" N VAL H 112 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL H 117 " --> pdb=" O MET H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 131 removed outlier: 3.641A pdb=" N GLU H 126 " --> pdb=" O GLY H 122 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY H 131 " --> pdb=" O CYS H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 142 removed outlier: 3.877A pdb=" N ILE H 141 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 150 removed outlier: 3.804A pdb=" N TRP H 150 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 156 removed outlier: 3.598A pdb=" N LYS H 155 " --> pdb=" O GLU H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 204 removed outlier: 3.778A pdb=" N LEU H 173 " --> pdb=" O GLU H 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER H 174 " --> pdb=" O GLU H 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU H 175 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN H 176 " --> pdb=" O LYS H 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN H 180 " --> pdb=" O GLN H 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 182 " --> pdb=" O GLN H 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE H 187 " --> pdb=" O GLY H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 247 removed outlier: 3.560A pdb=" N LYS H 221 " --> pdb=" O THR H 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS H 223 " --> pdb=" O ALA H 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU H 224 " --> pdb=" O GLN H 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN H 225 " --> pdb=" O LYS H 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN H 235 " --> pdb=" O LEU H 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE H 245 " --> pdb=" O ASN H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 265 Processing helix chain 'H' and resid 279 through 288 Processing helix chain 'I' and resid 2 through 8 Processing helix chain 'I' and resid 9 through 14 removed outlier: 3.767A pdb=" N GLN I 14 " --> pdb=" O PHE I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 38 removed outlier: 3.738A pdb=" N ILE I 18 " --> pdb=" O GLN I 14 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR I 20 " --> pdb=" O THR I 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 69 removed outlier: 3.618A pdb=" N PHE I 54 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU I 55 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE I 56 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Proline residue: I 58 - end of helix removed outlier: 3.561A pdb=" N PHE I 67 " --> pdb=" O LEU I 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU I 69 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 78 removed outlier: 3.957A pdb=" N TRP I 74 " --> pdb=" O ASN I 70 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE I 77 " --> pdb=" O SER I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 87 removed outlier: 3.612A pdb=" N VAL I 82 " --> pdb=" O GLY I 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN I 83 " --> pdb=" O CYS I 80 " (cutoff:3.500A) Proline residue: I 84 - end of helix Processing helix chain 'I' and resid 94 through 107 removed outlier: 3.559A pdb=" N TYR I 98 " --> pdb=" O CYS I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 121 removed outlier: 3.875A pdb=" N VAL I 112 " --> pdb=" O LEU I 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL I 117 " --> pdb=" O MET I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 131 removed outlier: 3.641A pdb=" N GLU I 126 " --> pdb=" O GLY I 122 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY I 131 " --> pdb=" O CYS I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 142 removed outlier: 3.877A pdb=" N ILE I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 150 removed outlier: 3.804A pdb=" N TRP I 150 " --> pdb=" O LYS I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 156 removed outlier: 3.599A pdb=" N LYS I 155 " --> pdb=" O GLU I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 204 removed outlier: 3.777A pdb=" N LEU I 173 " --> pdb=" O GLU I 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER I 174 " --> pdb=" O GLU I 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU I 175 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN I 176 " --> pdb=" O LYS I 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN I 178 " --> pdb=" O SER I 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN I 180 " --> pdb=" O GLN I 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU I 182 " --> pdb=" O GLN I 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE I 187 " --> pdb=" O GLY I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 247 removed outlier: 3.559A pdb=" N LYS I 221 " --> pdb=" O THR I 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS I 223 " --> pdb=" O ALA I 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU I 224 " --> pdb=" O GLN I 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN I 225 " --> pdb=" O LYS I 221 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN I 235 " --> pdb=" O LEU I 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS I 236 " --> pdb=" O ASP I 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE I 245 " --> pdb=" O ASN I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 265 Processing helix chain 'I' and resid 279 through 288 Processing helix chain 'J' and resid 2 through 8 Processing helix chain 'J' and resid 9 through 14 removed outlier: 3.766A pdb=" N GLN J 14 " --> pdb=" O PHE J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 38 removed outlier: 3.738A pdb=" N ILE J 18 " --> pdb=" O GLN J 14 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR J 20 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA J 24 " --> pdb=" O TYR J 20 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU J 33 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 69 removed outlier: 3.618A pdb=" N PHE J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU J 55 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Proline residue: J 58 - end of helix removed outlier: 3.561A pdb=" N PHE J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 78 removed outlier: 3.957A pdb=" N TRP J 74 " --> pdb=" O ASN J 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU J 76 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE J 77 " --> pdb=" O SER J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 87 removed outlier: 3.613A pdb=" N VAL J 82 " --> pdb=" O GLY J 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN J 83 " --> pdb=" O CYS J 80 " (cutoff:3.500A) Proline residue: J 84 - end of helix Processing helix chain 'J' and resid 94 through 107 removed outlier: 3.558A pdb=" N TYR J 98 " --> pdb=" O CYS J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 121 removed outlier: 3.875A pdb=" N VAL J 112 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL J 117 " --> pdb=" O MET J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 131 removed outlier: 3.641A pdb=" N GLU J 126 " --> pdb=" O GLY J 122 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY J 131 " --> pdb=" O CYS J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 142 removed outlier: 3.877A pdb=" N ILE J 141 " --> pdb=" O LEU J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 150 removed outlier: 3.804A pdb=" N TRP J 150 " --> pdb=" O LYS J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 156 removed outlier: 3.598A pdb=" N LYS J 155 " --> pdb=" O GLU J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 204 removed outlier: 3.777A pdb=" N LEU J 173 " --> pdb=" O GLU J 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER J 174 " --> pdb=" O GLU J 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU J 175 " --> pdb=" O LEU J 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN J 176 " --> pdb=" O LYS J 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN J 178 " --> pdb=" O SER J 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN J 180 " --> pdb=" O GLN J 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU J 182 " --> pdb=" O GLN J 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE J 187 " --> pdb=" O GLY J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 247 removed outlier: 3.559A pdb=" N LYS J 221 " --> pdb=" O THR J 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS J 223 " --> pdb=" O ALA J 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU J 224 " --> pdb=" O GLN J 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN J 225 " --> pdb=" O LYS J 221 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN J 235 " --> pdb=" O LEU J 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS J 236 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE J 245 " --> pdb=" O ASN J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 265 Processing helix chain 'J' and resid 279 through 288 Processing helix chain 'K' and resid 2 through 8 Processing helix chain 'K' and resid 9 through 14 removed outlier: 3.767A pdb=" N GLN K 14 " --> pdb=" O PHE K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 38 removed outlier: 3.738A pdb=" N ILE K 18 " --> pdb=" O GLN K 14 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA K 24 " --> pdb=" O TYR K 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU K 33 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 69 removed outlier: 3.618A pdb=" N PHE K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE K 56 " --> pdb=" O LEU K 52 " (cutoff:3.500A) Proline residue: K 58 - end of helix removed outlier: 3.561A pdb=" N PHE K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU K 69 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 78 removed outlier: 3.957A pdb=" N TRP K 74 " --> pdb=" O ASN K 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU K 76 " --> pdb=" O ARG K 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE K 77 " --> pdb=" O SER K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 87 removed outlier: 3.612A pdb=" N VAL K 82 " --> pdb=" O GLY K 79 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN K 83 " --> pdb=" O CYS K 80 " (cutoff:3.500A) Proline residue: K 84 - end of helix Processing helix chain 'K' and resid 94 through 107 removed outlier: 3.559A pdb=" N TYR K 98 " --> pdb=" O CYS K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 121 removed outlier: 3.875A pdb=" N VAL K 112 " --> pdb=" O LEU K 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 131 removed outlier: 3.641A pdb=" N GLU K 126 " --> pdb=" O GLY K 122 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY K 131 " --> pdb=" O CYS K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 142 removed outlier: 3.876A pdb=" N ILE K 141 " --> pdb=" O LEU K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 150 removed outlier: 3.804A pdb=" N TRP K 150 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 156 removed outlier: 3.598A pdb=" N LYS K 155 " --> pdb=" O GLU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 204 removed outlier: 3.778A pdb=" N LEU K 173 " --> pdb=" O GLU K 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER K 174 " --> pdb=" O GLU K 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU K 175 " --> pdb=" O LEU K 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN K 176 " --> pdb=" O LYS K 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN K 178 " --> pdb=" O SER K 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN K 180 " --> pdb=" O GLN K 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU K 182 " --> pdb=" O GLN K 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE K 187 " --> pdb=" O GLY K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 247 removed outlier: 3.560A pdb=" N LYS K 221 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS K 223 " --> pdb=" O ALA K 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU K 224 " --> pdb=" O GLN K 220 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN K 225 " --> pdb=" O LYS K 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN K 235 " --> pdb=" O LEU K 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS K 236 " --> pdb=" O ASP K 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE K 245 " --> pdb=" O ASN K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 265 Processing helix chain 'K' and resid 279 through 288 1364 hydrogen bonds defined for protein. 3993 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.67 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3960 1.31 - 1.43: 7954 1.43 - 1.56: 15047 1.56 - 1.69: 55 1.69 - 1.82: 286 Bond restraints: 27302 Sorted by residual: bond pdb=" C12 PA8 G 303 " pdb=" O7 PA8 G 303 " ideal model delta sigma weight residual 1.327 1.404 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C12 PA8 B 303 " pdb=" O7 PA8 B 303 " ideal model delta sigma weight residual 1.327 1.404 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C4 PA8 G 305 " pdb=" O5 PA8 G 305 " ideal model delta sigma weight residual 1.327 1.404 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C12 PA8 A 305 " pdb=" O7 PA8 A 305 " ideal model delta sigma weight residual 1.327 1.404 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C12 PA8 C 303 " pdb=" O7 PA8 C 303 " ideal model delta sigma weight residual 1.327 1.404 -0.077 2.00e-02 2.50e+03 1.48e+01 ... (remaining 27297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 34853 2.15 - 4.31: 1196 4.31 - 6.46: 442 6.46 - 8.62: 161 8.62 - 10.77: 121 Bond angle restraints: 36773 Sorted by residual: angle pdb=" N ILE A 87 " pdb=" CA ILE A 87 " pdb=" C ILE A 87 " ideal model delta sigma weight residual 113.42 107.17 6.25 1.17e+00 7.31e-01 2.85e+01 angle pdb=" N ILE K 87 " pdb=" CA ILE K 87 " pdb=" C ILE K 87 " ideal model delta sigma weight residual 113.42 107.20 6.22 1.17e+00 7.31e-01 2.83e+01 angle pdb=" N ILE D 87 " pdb=" CA ILE D 87 " pdb=" C ILE D 87 " ideal model delta sigma weight residual 113.42 107.20 6.22 1.17e+00 7.31e-01 2.82e+01 angle pdb=" N ILE H 87 " pdb=" CA ILE H 87 " pdb=" C ILE H 87 " ideal model delta sigma weight residual 113.42 107.20 6.22 1.17e+00 7.31e-01 2.82e+01 angle pdb=" N ILE G 87 " pdb=" CA ILE G 87 " pdb=" C ILE G 87 " ideal model delta sigma weight residual 113.42 107.21 6.21 1.17e+00 7.31e-01 2.82e+01 ... (remaining 36768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 13616 16.88 - 33.77: 1861 33.77 - 50.65: 407 50.65 - 67.54: 77 67.54 - 84.42: 44 Dihedral angle restraints: 16005 sinusoidal: 6743 harmonic: 9262 Sorted by residual: dihedral pdb=" CA LYS D 221 " pdb=" C LYS D 221 " pdb=" N GLU D 222 " pdb=" CA GLU D 222 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LYS E 221 " pdb=" C LYS E 221 " pdb=" N GLU E 222 " pdb=" CA GLU E 222 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LYS C 221 " pdb=" C LYS C 221 " pdb=" N GLU C 222 " pdb=" CA GLU C 222 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 16002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2335 0.041 - 0.082: 1261 0.082 - 0.123: 238 0.123 - 0.164: 49 0.164 - 0.205: 33 Chirality restraints: 3916 Sorted by residual: chirality pdb=" CA PRO D 165 " pdb=" N PRO D 165 " pdb=" C PRO D 165 " pdb=" CB PRO D 165 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO K 165 " pdb=" N PRO K 165 " pdb=" C PRO K 165 " pdb=" CB PRO K 165 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PRO E 165 " pdb=" N PRO E 165 " pdb=" C PRO E 165 " pdb=" CB PRO E 165 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3913 not shown) Planarity restraints: 4499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA J 110 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO J 111 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO J 111 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO J 111 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 110 " 0.048 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO C 111 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 111 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 111 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 110 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO G 111 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO G 111 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 111 " -0.040 5.00e-02 4.00e+02 ... (remaining 4496 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 9644 2.90 - 3.40: 22376 3.40 - 3.90: 39472 3.90 - 4.40: 47404 4.40 - 4.90: 81961 Nonbonded interactions: 200857 Sorted by model distance: nonbonded pdb=" O LEU A 231 " pdb=" NZ LYS K 221 " model vdw 2.395 3.120 nonbonded pdb=" NZ LYS B 221 " pdb=" O LEU C 231 " model vdw 2.401 3.120 nonbonded pdb=" NZ LYS A 221 " pdb=" O LEU B 231 " model vdw 2.404 3.120 nonbonded pdb=" NZ LYS E 221 " pdb=" O LEU F 231 " model vdw 2.405 3.120 nonbonded pdb=" NZ LYS I 221 " pdb=" O LEU J 231 " model vdw 2.409 3.120 ... (remaining 200852 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.140 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 0.077 27335 Z= 0.412 Angle : 1.223 10.774 36839 Z= 0.534 Chirality : 0.051 0.205 3916 Planarity : 0.007 0.072 4499 Dihedral : 16.352 84.422 9900 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.95 (0.08), residues: 3146 helix: -4.81 (0.03), residues: 2409 sheet: None (None), residues: 0 loop : -2.59 (0.19), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 204 TYR 0.012 0.002 TYR E 209 PHE 0.017 0.002 PHE B 68 TRP 0.018 0.002 TRP H 262 HIS 0.004 0.001 HIS B 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00879 / 0.41 (27302) covalent geometry : angle 1.22094 / 0.53 (36773) SS BOND : bond 0.00556 / 0.36 ( 33) SS BOND : angle 1.99814 / 1.42 ( 66) hydrogen bonds : bond 0.38954 / 24.90 ( 1364) hydrogen bonds : angle 10.77795 / 7.30 ( 3993) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 721 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8483 (t80) cc_final: 0.8202 (t80) REVERT: A 32 ARG cc_start: 0.8503 (mmm160) cc_final: 0.8098 (mmp80) REVERT: A 283 ARG cc_start: 0.8291 (ttp80) cc_final: 0.8082 (ttp-110) REVERT: B 8 LEU cc_start: 0.7319 (mt) cc_final: 0.6916 (tt) REVERT: B 32 ARG cc_start: 0.8358 (mmm160) cc_final: 0.7941 (mmp80) REVERT: B 88 PHE cc_start: 0.7083 (m-80) cc_final: 0.6772 (m-80) REVERT: C 8 LEU cc_start: 0.7197 (mt) cc_final: 0.6860 (tt) REVERT: C 32 ARG cc_start: 0.8411 (mmm160) cc_final: 0.8167 (mmp80) REVERT: C 88 PHE cc_start: 0.7154 (m-80) cc_final: 0.6933 (m-80) REVERT: C 169 GLU cc_start: 0.7655 (tp30) cc_final: 0.7396 (tm-30) REVERT: C 276 GLN cc_start: 0.8050 (pt0) cc_final: 0.7676 (mt0) REVERT: C 283 ARG cc_start: 0.8321 (ttp80) cc_final: 0.8100 (ttp-170) REVERT: D 88 PHE cc_start: 0.6987 (m-80) cc_final: 0.6750 (m-80) REVERT: D 267 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7867 (mt-10) REVERT: E 32 ARG cc_start: 0.8375 (mmm160) cc_final: 0.8071 (mmp80) REVERT: E 88 PHE cc_start: 0.7209 (m-80) cc_final: 0.6876 (m-80) REVERT: E 169 GLU cc_start: 0.7695 (tp30) cc_final: 0.7478 (tm-30) REVERT: E 202 ARG cc_start: 0.7820 (mmm-85) cc_final: 0.7580 (mmt180) REVERT: E 283 ARG cc_start: 0.8344 (ttp80) cc_final: 0.8121 (ttp-170) REVERT: F 202 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7707 (mmt180) REVERT: F 233 TYR cc_start: 0.8795 (m-80) cc_final: 0.8578 (m-80) REVERT: F 267 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7835 (mt-10) REVERT: G 8 LEU cc_start: 0.6958 (mt) cc_final: 0.6530 (tt) REVERT: G 30 SER cc_start: 0.8812 (t) cc_final: 0.8606 (m) REVERT: G 169 GLU cc_start: 0.7673 (tp30) cc_final: 0.7426 (tm-30) REVERT: H 95 ARG cc_start: 0.7314 (ttt90) cc_final: 0.7083 (ttt90) REVERT: H 220 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7724 (tp-100) REVERT: H 283 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8166 (ttp-170) REVERT: I 8 LEU cc_start: 0.6954 (mt) cc_final: 0.6535 (tt) REVERT: I 88 PHE cc_start: 0.7097 (m-80) cc_final: 0.6829 (m-80) REVERT: I 97 PHE cc_start: 0.8449 (m-80) cc_final: 0.8194 (m-80) REVERT: I 202 ARG cc_start: 0.7906 (mmm-85) cc_final: 0.7568 (mmt180) REVERT: I 233 TYR cc_start: 0.8754 (m-80) cc_final: 0.8542 (m-80) REVERT: I 283 ARG cc_start: 0.8276 (ttp80) cc_final: 0.8006 (ttp-170) REVERT: J 46 GLU cc_start: 0.7260 (pt0) cc_final: 0.6969 (pp20) REVERT: J 283 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7993 (ttp-170) REVERT: K 8 LEU cc_start: 0.7135 (mt) cc_final: 0.6725 (tt) REVERT: K 88 PHE cc_start: 0.7077 (m-80) cc_final: 0.6838 (m-80) REVERT: K 169 GLU cc_start: 0.7592 (tp30) cc_final: 0.7344 (tm-30) REVERT: K 220 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7847 (tp-100) REVERT: K 276 GLN cc_start: 0.8205 (pt0) cc_final: 0.7951 (mt0) REVERT: K 283 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8061 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 721 average time/residue: 0.7740 time to fit residues: 629.2422 Evaluate side-chains 491 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.0270 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN A 178 GLN A 248 ASN B 83 ASN B 168 ASN B 248 ASN B 276 GLN C 83 ASN C 225 GLN C 248 ASN C 287 ASN D 83 ASN D 248 ASN E 102 GLN E 176 GLN E 248 ASN E 276 GLN F 168 ASN F 225 GLN F 248 ASN G 102 GLN G 178 GLN G 220 GLN G 248 ASN H 83 ASN H 276 GLN I 83 ASN I 248 ASN I 273 GLN I 276 GLN J 83 ASN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 ASN K 83 ASN K 178 GLN K 248 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.159943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115877 restraints weight = 27564.399| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.01 r_work: 0.3147 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 27335 Z= 0.121 Angle : 0.567 7.897 36839 Z= 0.301 Chirality : 0.036 0.160 3916 Planarity : 0.005 0.044 4499 Dihedral : 10.576 59.190 3982 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.00 % Allowed : 13.56 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.13), residues: 3146 helix: -1.98 (0.09), residues: 2387 sheet: None (None), residues: 0 loop : -1.70 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 95 TYR 0.017 0.001 TYR A 98 PHE 0.017 0.001 PHE C 214 TRP 0.013 0.001 TRP E 60 HIS 0.001 0.000 HIS C 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (27302) covalent geometry : angle 0.56557 / 0.30 (36773) SS BOND : bond 0.00195 / 0.12 ( 33) SS BOND : angle 1.18960 / 0.90 ( 66) hydrogen bonds : bond 0.06318 / 4.03 ( 1364) hydrogen bonds : angle 3.95652 / 2.68 ( 3993) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 466 time to evaluate : 0.977 Fit side-chains REVERT: A 30 SER cc_start: 0.7964 (t) cc_final: 0.7607 (m) REVERT: A 95 ARG cc_start: 0.6987 (ttt90) cc_final: 0.6311 (ttt90) REVERT: A 249 LYS cc_start: 0.8160 (mttt) cc_final: 0.7898 (mttp) REVERT: B 30 SER cc_start: 0.7959 (t) cc_final: 0.7654 (p) REVERT: B 88 PHE cc_start: 0.6953 (m-80) cc_final: 0.6674 (m-80) REVERT: C 147 LYS cc_start: 0.7453 (tptp) cc_final: 0.7232 (ttpp) REVERT: C 169 GLU cc_start: 0.8243 (tp30) cc_final: 0.7604 (tm-30) REVERT: C 276 GLN cc_start: 0.8218 (pt0) cc_final: 0.7655 (mt0) REVERT: D 30 SER cc_start: 0.7799 (t) cc_final: 0.7553 (p) REVERT: E 88 PHE cc_start: 0.6987 (m-80) cc_final: 0.6675 (m-80) REVERT: E 169 GLU cc_start: 0.8391 (tp30) cc_final: 0.7522 (tm-30) REVERT: E 194 SER cc_start: 0.8785 (t) cc_final: 0.8575 (p) REVERT: F 169 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7513 (tp30) REVERT: F 249 LYS cc_start: 0.8071 (mttt) cc_final: 0.7849 (mttp) REVERT: F 267 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8338 (mt-10) REVERT: G 12 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7488 (mm) REVERT: G 30 SER cc_start: 0.8212 (t) cc_final: 0.7925 (p) REVERT: G 88 PHE cc_start: 0.6801 (m-80) cc_final: 0.6568 (m-80) REVERT: G 133 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7829 (tpp-160) REVERT: G 147 LYS cc_start: 0.7457 (tptt) cc_final: 0.7255 (ttpp) REVERT: G 169 GLU cc_start: 0.8267 (tp30) cc_final: 0.7344 (tm-30) REVERT: G 220 GLN cc_start: 0.8239 (tp40) cc_final: 0.8000 (tm-30) REVERT: H 30 SER cc_start: 0.7963 (OUTLIER) cc_final: 0.7563 (p) REVERT: H 95 ARG cc_start: 0.6808 (ttt90) cc_final: 0.6525 (ttt90) REVERT: H 147 LYS cc_start: 0.7335 (tptp) cc_final: 0.7121 (ttpp) REVERT: I 30 SER cc_start: 0.8138 (t) cc_final: 0.7897 (p) REVERT: I 97 PHE cc_start: 0.8364 (m-80) cc_final: 0.8109 (m-80) REVERT: I 194 SER cc_start: 0.8749 (t) cc_final: 0.8542 (p) REVERT: J 30 SER cc_start: 0.8097 (t) cc_final: 0.7827 (p) REVERT: J 169 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7647 (tm-30) REVERT: J 220 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8130 (tp40) REVERT: K 30 SER cc_start: 0.8075 (t) cc_final: 0.7708 (p) REVERT: K 31 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7396 (tm-30) REVERT: K 88 PHE cc_start: 0.6920 (m-80) cc_final: 0.6692 (m-80) REVERT: K 129 MET cc_start: 0.8767 (tpp) cc_final: 0.8453 (mmt) REVERT: K 169 GLU cc_start: 0.8248 (tp30) cc_final: 0.7389 (tm-30) REVERT: K 276 GLN cc_start: 0.8342 (pt0) cc_final: 0.7888 (mt0) outliers start: 56 outliers final: 22 residues processed: 503 average time/residue: 0.6839 time to fit residues: 392.4491 Evaluate side-chains 439 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 414 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain I residue 13 ASN Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 152 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 9.9990 chunk 277 optimal weight: 0.0040 chunk 176 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 0.3980 chunk 306 optimal weight: 6.9990 chunk 291 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 102 GLN E 176 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN G 168 ASN G 276 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 168 ASN H 276 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN I 273 GLN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 ASN J 176 GLN J 178 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115788 restraints weight = 27768.556| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.97 r_work: 0.3146 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27335 Z= 0.108 Angle : 0.516 8.967 36839 Z= 0.267 Chirality : 0.036 0.170 3916 Planarity : 0.004 0.040 4499 Dihedral : 9.791 58.522 3982 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.11 % Allowed : 16.25 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.15), residues: 3146 helix: -0.06 (0.11), residues: 2255 sheet: None (None), residues: 0 loop : -1.53 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 95 TYR 0.014 0.001 TYR D 98 PHE 0.011 0.001 PHE E 214 TRP 0.010 0.001 TRP G 60 HIS 0.002 0.000 HIS I 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (27302) covalent geometry : angle 0.51440 / 0.27 (36773) SS BOND : bond 0.00318 / 0.19 ( 33) SS BOND : angle 1.20744 / 0.95 ( 66) hydrogen bonds : bond 0.05412 / 3.44 ( 1364) hydrogen bonds : angle 3.28207 / 2.23 ( 3993) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 423 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7922 (mt) cc_final: 0.7638 (OUTLIER) REVERT: A 30 SER cc_start: 0.8265 (t) cc_final: 0.7896 (m) REVERT: A 95 ARG cc_start: 0.7032 (ttt90) cc_final: 0.6439 (ttt90) REVERT: A 200 TYR cc_start: 0.8384 (t80) cc_final: 0.8125 (t80) REVERT: A 249 LYS cc_start: 0.7991 (mttt) cc_final: 0.7749 (mttp) REVERT: A 283 ARG cc_start: 0.8903 (ttp80) cc_final: 0.8632 (ttp-170) REVERT: B 30 SER cc_start: 0.8063 (t) cc_final: 0.7767 (p) REVERT: B 88 PHE cc_start: 0.7002 (m-80) cc_final: 0.6765 (m-80) REVERT: B 95 ARG cc_start: 0.7156 (ttt90) cc_final: 0.6630 (ttt90) REVERT: C 147 LYS cc_start: 0.7429 (tptp) cc_final: 0.7213 (ttpp) REVERT: C 169 GLU cc_start: 0.8275 (tp30) cc_final: 0.7569 (tm-30) REVERT: C 249 LYS cc_start: 0.7987 (mttt) cc_final: 0.7753 (mttp) REVERT: C 276 GLN cc_start: 0.8265 (pt0) cc_final: 0.7767 (mt0) REVERT: D 30 SER cc_start: 0.7934 (t) cc_final: 0.7653 (p) REVERT: D 249 LYS cc_start: 0.7836 (mttt) cc_final: 0.7609 (mtpp) REVERT: E 88 PHE cc_start: 0.6918 (m-80) cc_final: 0.6643 (m-80) REVERT: E 169 GLU cc_start: 0.8346 (tp30) cc_final: 0.7474 (tm-30) REVERT: E 276 GLN cc_start: 0.7714 (pt0) cc_final: 0.7482 (mt0) REVERT: F 26 LEU cc_start: 0.8239 (mt) cc_final: 0.8009 (mp) REVERT: F 169 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7481 (tp30) REVERT: F 267 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8341 (mt-10) REVERT: G 12 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7253 (mm) REVERT: G 30 SER cc_start: 0.8359 (t) cc_final: 0.8052 (p) REVERT: G 147 LYS cc_start: 0.7627 (tptt) cc_final: 0.7380 (ttpp) REVERT: G 169 GLU cc_start: 0.8167 (tp30) cc_final: 0.7319 (tm-30) REVERT: G 220 GLN cc_start: 0.8304 (tp40) cc_final: 0.8081 (tm-30) REVERT: H 30 SER cc_start: 0.8056 (t) cc_final: 0.7828 (p) REVERT: H 95 ARG cc_start: 0.6851 (ttt90) cc_final: 0.6368 (ttt90) REVERT: H 169 GLU cc_start: 0.7831 (tp30) cc_final: 0.7410 (tp30) REVERT: H 276 GLN cc_start: 0.8188 (pt0) cc_final: 0.7850 (mt0) REVERT: I 25 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7298 (mt) REVERT: I 30 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.8010 (p) REVERT: I 97 PHE cc_start: 0.8360 (m-80) cc_final: 0.8100 (m-80) REVERT: I 163 MET cc_start: 0.7587 (ttp) cc_final: 0.7297 (ttm) REVERT: I 202 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7924 (mmt180) REVERT: I 249 LYS cc_start: 0.7805 (mttt) cc_final: 0.7590 (mttp) REVERT: I 283 ARG cc_start: 0.8857 (ttp80) cc_final: 0.8531 (ttp-170) REVERT: J 72 ARG cc_start: 0.8599 (ttm170) cc_final: 0.8279 (ttp-170) REVERT: J 169 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7479 (tp30) REVERT: J 220 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8069 (tp40) REVERT: K 31 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7627 (tm-30) REVERT: K 129 MET cc_start: 0.8817 (tpp) cc_final: 0.8548 (mmt) REVERT: K 133 ARG cc_start: 0.7967 (tpp-160) cc_final: 0.7724 (tpp-160) REVERT: K 169 GLU cc_start: 0.8209 (tp30) cc_final: 0.7277 (tm-30) REVERT: K 276 GLN cc_start: 0.8331 (pt0) cc_final: 0.7894 (mt0) outliers start: 59 outliers final: 21 residues processed: 456 average time/residue: 0.6596 time to fit residues: 341.7342 Evaluate side-chains 407 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 384 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 152 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 65 optimal weight: 0.0970 chunk 278 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 276 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 290 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN B 102 GLN C 102 GLN C 178 GLN D 176 GLN E 102 GLN E 176 GLN E 273 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN F 273 GLN G 102 GLN G 273 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 273 GLN I 102 GLN I 273 GLN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 176 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN K 176 GLN K 273 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.159045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116032 restraints weight = 28198.203| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.89 r_work: 0.3173 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 27335 Z= 0.109 Angle : 0.505 8.504 36839 Z= 0.260 Chirality : 0.036 0.176 3916 Planarity : 0.003 0.040 4499 Dihedral : 9.499 59.794 3982 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.19 % Allowed : 16.25 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.16), residues: 3146 helix: 0.54 (0.11), residues: 2288 sheet: None (None), residues: 0 loop : -1.38 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 95 TYR 0.017 0.001 TYR K 98 PHE 0.013 0.001 PHE D 214 TRP 0.010 0.001 TRP E 60 HIS 0.002 0.000 HIS I 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (27302) covalent geometry : angle 0.50281 / 0.26 (36773) SS BOND : bond 0.00230 / 0.15 ( 33) SS BOND : angle 1.19964 / 0.89 ( 66) hydrogen bonds : bond 0.05359 / 3.41 ( 1364) hydrogen bonds : angle 3.12708 / 2.13 ( 3993) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 397 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8090 (t80) cc_final: 0.7888 (t80) REVERT: A 30 SER cc_start: 0.8471 (t) cc_final: 0.8138 (p) REVERT: A 200 TYR cc_start: 0.8472 (t80) cc_final: 0.8216 (t80) REVERT: B 30 SER cc_start: 0.8313 (t) cc_final: 0.8063 (p) REVERT: B 88 PHE cc_start: 0.6975 (m-80) cc_final: 0.6756 (m-80) REVERT: B 95 ARG cc_start: 0.7160 (ttt90) cc_final: 0.6522 (ttt90) REVERT: B 149 CYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6040 (t) REVERT: C 169 GLU cc_start: 0.8179 (tp30) cc_final: 0.7186 (tp30) REVERT: C 249 LYS cc_start: 0.8009 (mttt) cc_final: 0.7808 (mttp) REVERT: C 276 GLN cc_start: 0.8203 (pt0) cc_final: 0.7671 (mt0) REVERT: D 30 SER cc_start: 0.8068 (t) cc_final: 0.7825 (p) REVERT: E 88 PHE cc_start: 0.7011 (m-80) cc_final: 0.6781 (m-80) REVERT: E 169 GLU cc_start: 0.8345 (tp30) cc_final: 0.7427 (tm-30) REVERT: E 276 GLN cc_start: 0.7785 (pt0) cc_final: 0.7545 (mt0) REVERT: F 26 LEU cc_start: 0.8415 (mt) cc_final: 0.8210 (mp) REVERT: F 169 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7480 (tp30) REVERT: F 267 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8350 (mt-10) REVERT: F 276 GLN cc_start: 0.8209 (pt0) cc_final: 0.7763 (mt0) REVERT: G 30 SER cc_start: 0.8462 (t) cc_final: 0.8141 (p) REVERT: G 147 LYS cc_start: 0.7702 (tptt) cc_final: 0.7482 (ttpp) REVERT: G 169 GLU cc_start: 0.8048 (tp30) cc_final: 0.7436 (tm-30) REVERT: G 220 GLN cc_start: 0.8351 (tp40) cc_final: 0.8059 (tm-30) REVERT: H 23 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7837 (ttp) REVERT: H 95 ARG cc_start: 0.6827 (ttt90) cc_final: 0.6292 (ttt90) REVERT: H 169 GLU cc_start: 0.7756 (tp30) cc_final: 0.7325 (tp30) REVERT: H 276 GLN cc_start: 0.8192 (pt0) cc_final: 0.7869 (mt0) REVERT: I 25 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7408 (mt) REVERT: I 30 SER cc_start: 0.8451 (t) cc_final: 0.8203 (p) REVERT: I 97 PHE cc_start: 0.8433 (m-80) cc_final: 0.8166 (m-80) REVERT: I 149 CYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6747 (t) REVERT: I 163 MET cc_start: 0.7640 (ttp) cc_final: 0.7397 (ttm) REVERT: I 169 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7304 (tp30) REVERT: I 202 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7836 (mmt180) REVERT: I 249 LYS cc_start: 0.7868 (mttt) cc_final: 0.7542 (mtmm) REVERT: I 283 ARG cc_start: 0.8831 (ttp80) cc_final: 0.8508 (ttp-170) REVERT: J 23 MET cc_start: 0.8331 (ttm) cc_final: 0.7941 (ttp) REVERT: J 30 SER cc_start: 0.8421 (t) cc_final: 0.8218 (p) REVERT: J 72 ARG cc_start: 0.8631 (ttm170) cc_final: 0.8350 (ttp80) REVERT: J 169 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7496 (tp30) REVERT: J 220 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8086 (tp40) REVERT: J 276 GLN cc_start: 0.7955 (pt0) cc_final: 0.7598 (mt0) REVERT: K 129 MET cc_start: 0.8812 (tpp) cc_final: 0.8526 (mmt) REVERT: K 133 ARG cc_start: 0.8123 (tpp-160) cc_final: 0.7871 (tpp-160) REVERT: K 169 GLU cc_start: 0.8128 (tp30) cc_final: 0.7246 (tm-30) REVERT: K 276 GLN cc_start: 0.8353 (pt0) cc_final: 0.7989 (mt0) outliers start: 89 outliers final: 39 residues processed: 449 average time/residue: 0.7088 time to fit residues: 361.7632 Evaluate side-chains 415 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 372 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 94 CYS Chi-restraints excluded: chain K residue 152 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 294 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 196 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 128 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 219 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN B 273 GLN E 102 GLN E 176 GLN F 176 GLN F 273 GLN G 273 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 220 GLN H 273 GLN I 102 GLN I 273 GLN J 176 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 273 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.158351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115319 restraints weight = 28105.219| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.89 r_work: 0.3158 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27335 Z= 0.114 Angle : 0.508 8.525 36839 Z= 0.260 Chirality : 0.037 0.173 3916 Planarity : 0.003 0.041 4499 Dihedral : 9.388 59.846 3982 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.33 % Allowed : 16.86 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 3146 helix: 0.80 (0.11), residues: 2288 sheet: None (None), residues: 0 loop : -1.27 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 95 TYR 0.016 0.001 TYR E 98 PHE 0.013 0.001 PHE D 214 TRP 0.010 0.001 TRP E 60 HIS 0.002 0.000 HIS I 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (27302) covalent geometry : angle 0.50584 / 0.26 (36773) SS BOND : bond 0.00294 / 0.19 ( 33) SS BOND : angle 1.16320 / 0.84 ( 66) hydrogen bonds : bond 0.05478 / 3.48 ( 1364) hydrogen bonds : angle 3.08509 / 2.10 ( 3993) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 380 time to evaluate : 0.788 Fit side-chains REVERT: A 12 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.6986 (mm) REVERT: A 22 PHE cc_start: 0.8058 (t80) cc_final: 0.7822 (t80) REVERT: A 95 ARG cc_start: 0.7214 (ttt90) cc_final: 0.6870 (ttt90) REVERT: A 200 TYR cc_start: 0.8493 (t80) cc_final: 0.8250 (t80) REVERT: B 30 SER cc_start: 0.8295 (t) cc_final: 0.8018 (p) REVERT: B 95 ARG cc_start: 0.7165 (ttt90) cc_final: 0.6588 (ttt90) REVERT: B 149 CYS cc_start: 0.6724 (OUTLIER) cc_final: 0.6500 (t) REVERT: C 12 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7205 (mm) REVERT: C 149 CYS cc_start: 0.6739 (OUTLIER) cc_final: 0.6323 (t) REVERT: C 169 GLU cc_start: 0.8182 (tp30) cc_final: 0.7240 (tp30) REVERT: C 249 LYS cc_start: 0.7995 (mttt) cc_final: 0.7792 (mttp) REVERT: C 276 GLN cc_start: 0.8205 (pt0) cc_final: 0.7682 (mt0) REVERT: D 12 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7177 (mm) REVERT: D 30 SER cc_start: 0.8093 (t) cc_final: 0.7834 (p) REVERT: E 12 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7304 (mm) REVERT: E 88 PHE cc_start: 0.6989 (m-80) cc_final: 0.6787 (m-80) REVERT: E 169 GLU cc_start: 0.8364 (tp30) cc_final: 0.7464 (tm-30) REVERT: F 12 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7278 (mm) REVERT: F 26 LEU cc_start: 0.8393 (mt) cc_final: 0.8178 (mp) REVERT: F 169 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7435 (tp30) REVERT: F 267 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8349 (mt-10) REVERT: F 276 GLN cc_start: 0.8198 (pt0) cc_final: 0.7766 (mt0) REVERT: G 102 GLN cc_start: 0.8405 (tt0) cc_final: 0.8176 (tt0) REVERT: G 147 LYS cc_start: 0.7687 (tptt) cc_final: 0.7464 (ttpp) REVERT: G 169 GLU cc_start: 0.7995 (tp30) cc_final: 0.7455 (tm-30) REVERT: H 30 SER cc_start: 0.8242 (t) cc_final: 0.8008 (p) REVERT: H 95 ARG cc_start: 0.6830 (ttt90) cc_final: 0.6264 (ttt90) REVERT: H 169 GLU cc_start: 0.7798 (tp30) cc_final: 0.7359 (tp30) REVERT: H 276 GLN cc_start: 0.8206 (pt0) cc_final: 0.7890 (mt0) REVERT: I 12 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7311 (mm) REVERT: I 25 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7488 (mt) REVERT: I 30 SER cc_start: 0.8421 (t) cc_final: 0.8169 (p) REVERT: I 97 PHE cc_start: 0.8425 (m-80) cc_final: 0.8142 (m-80) REVERT: I 149 CYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6702 (t) REVERT: I 163 MET cc_start: 0.7600 (ttp) cc_final: 0.7360 (ttm) REVERT: I 169 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7419 (tp30) REVERT: I 249 LYS cc_start: 0.7881 (mttt) cc_final: 0.7554 (mtmm) REVERT: J 12 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7177 (mm) REVERT: J 30 SER cc_start: 0.8471 (t) cc_final: 0.8267 (p) REVERT: J 72 ARG cc_start: 0.8652 (ttm170) cc_final: 0.8372 (ttp80) REVERT: J 169 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7511 (tp30) REVERT: J 220 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8129 (tp40) REVERT: J 276 GLN cc_start: 0.7949 (pt0) cc_final: 0.7565 (mt0) REVERT: K 12 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7308 (mm) REVERT: K 129 MET cc_start: 0.8787 (tpp) cc_final: 0.8498 (mmt) REVERT: K 133 ARG cc_start: 0.8065 (tpp-160) cc_final: 0.7865 (tpp-160) REVERT: K 169 GLU cc_start: 0.8237 (tp30) cc_final: 0.7367 (tm-30) REVERT: K 276 GLN cc_start: 0.8314 (pt0) cc_final: 0.7965 (mt0) outliers start: 93 outliers final: 57 residues processed: 443 average time/residue: 0.6539 time to fit residues: 331.7160 Evaluate side-chains 440 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 371 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 176 GLN Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain K residue 231 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 279 optimal weight: 6.9990 chunk 292 optimal weight: 0.6980 chunk 237 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 223 optimal weight: 9.9990 chunk 263 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 275 optimal weight: 0.8980 chunk 224 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 165 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN D 273 GLN E 102 GLN E 176 GLN E 276 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN F 273 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 168 ASN G 220 GLN G 273 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 273 GLN I 102 GLN I 273 GLN J 176 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 273 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.159211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116182 restraints weight = 28223.860| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.89 r_work: 0.3177 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27335 Z= 0.104 Angle : 0.494 8.835 36839 Z= 0.253 Chirality : 0.036 0.174 3916 Planarity : 0.003 0.037 4499 Dihedral : 9.152 59.851 3982 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.19 % Allowed : 17.68 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 3146 helix: 1.00 (0.11), residues: 2299 sheet: None (None), residues: 0 loop : -1.12 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.016 0.001 TYR C 98 PHE 0.015 0.001 PHE A 214 TRP 0.010 0.001 TRP E 60 HIS 0.001 0.000 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (27302) covalent geometry : angle 0.49266 / 0.25 (36773) SS BOND : bond 0.00254 / 0.16 ( 33) SS BOND : angle 0.97199 / 0.70 ( 66) hydrogen bonds : bond 0.05042 / 3.20 ( 1364) hydrogen bonds : angle 3.02306 / 2.06 ( 3993) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 370 time to evaluate : 0.875 Fit side-chains REVERT: A 12 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6980 (mm) REVERT: A 22 PHE cc_start: 0.8075 (t80) cc_final: 0.7860 (t80) REVERT: A 95 ARG cc_start: 0.7248 (ttt90) cc_final: 0.6904 (ttt90) REVERT: A 200 TYR cc_start: 0.8455 (t80) cc_final: 0.8181 (t80) REVERT: B 12 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7303 (mm) REVERT: B 30 SER cc_start: 0.8315 (t) cc_final: 0.8037 (p) REVERT: B 163 MET cc_start: 0.6932 (ttp) cc_final: 0.6725 (ttm) REVERT: C 12 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7203 (mm) REVERT: C 169 GLU cc_start: 0.8144 (tp30) cc_final: 0.7583 (tm-30) REVERT: C 276 GLN cc_start: 0.8206 (pt0) cc_final: 0.7697 (mt0) REVERT: D 12 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7191 (mm) REVERT: D 30 SER cc_start: 0.8083 (t) cc_final: 0.7805 (p) REVERT: D 220 GLN cc_start: 0.8247 (tm-30) cc_final: 0.8006 (tp40) REVERT: E 12 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7317 (mm) REVERT: E 169 GLU cc_start: 0.8381 (tp30) cc_final: 0.7467 (tm-30) REVERT: E 276 GLN cc_start: 0.7788 (pt0) cc_final: 0.7544 (mt0) REVERT: F 12 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7274 (mm) REVERT: F 26 LEU cc_start: 0.8530 (mt) cc_final: 0.8314 (mp) REVERT: F 169 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7455 (tp30) REVERT: F 267 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8324 (mt-10) REVERT: F 276 GLN cc_start: 0.8190 (pt0) cc_final: 0.7770 (mt0) REVERT: G 147 LYS cc_start: 0.7610 (tptt) cc_final: 0.7366 (OUTLIER) REVERT: G 169 GLU cc_start: 0.7953 (tp30) cc_final: 0.7404 (tm-30) REVERT: H 12 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7351 (mm) REVERT: H 30 SER cc_start: 0.8194 (t) cc_final: 0.7990 (p) REVERT: H 95 ARG cc_start: 0.6809 (ttt90) cc_final: 0.6233 (ttt90) REVERT: H 169 GLU cc_start: 0.7794 (tp30) cc_final: 0.7341 (tp30) REVERT: H 276 GLN cc_start: 0.8197 (pt0) cc_final: 0.7885 (mt0) REVERT: I 12 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7293 (mm) REVERT: I 25 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7496 (mt) REVERT: I 30 SER cc_start: 0.8380 (t) cc_final: 0.8119 (p) REVERT: I 97 PHE cc_start: 0.8402 (m-80) cc_final: 0.8126 (m-80) REVERT: I 149 CYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6458 (t) REVERT: I 163 MET cc_start: 0.7598 (ttp) cc_final: 0.7318 (ttm) REVERT: I 169 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7399 (tp30) REVERT: I 249 LYS cc_start: 0.7828 (mttt) cc_final: 0.7485 (mtmm) REVERT: J 12 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7112 (mm) REVERT: J 72 ARG cc_start: 0.8616 (ttm170) cc_final: 0.8337 (ttp80) REVERT: J 169 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7477 (tp30) REVERT: J 220 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8092 (tp40) REVERT: J 276 GLN cc_start: 0.7952 (pt0) cc_final: 0.7580 (mt0) REVERT: K 12 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7347 (mm) REVERT: K 25 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7464 (mt) REVERT: K 30 SER cc_start: 0.8312 (t) cc_final: 0.7984 (p) REVERT: K 129 MET cc_start: 0.8769 (tpp) cc_final: 0.8515 (mmt) REVERT: K 169 GLU cc_start: 0.8217 (tp30) cc_final: 0.7342 (tm-30) REVERT: K 276 GLN cc_start: 0.8316 (pt0) cc_final: 0.7914 (mt0) outliers start: 89 outliers final: 56 residues processed: 426 average time/residue: 0.6211 time to fit residues: 303.6928 Evaluate side-chains 429 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 361 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 94 CYS Chi-restraints excluded: chain K residue 231 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 140 optimal weight: 8.9990 chunk 194 optimal weight: 0.6980 chunk 280 optimal weight: 0.7980 chunk 290 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 chunk 222 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN A 273 GLN B 273 GLN D 273 GLN E 102 GLN E 176 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN F 273 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 273 GLN H 102 GLN H 220 GLN H 273 GLN I 102 GLN I 273 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 ASN K 176 GLN K 273 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.158279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115362 restraints weight = 27969.413| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.88 r_work: 0.3160 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27335 Z= 0.111 Angle : 0.500 9.085 36839 Z= 0.256 Chirality : 0.037 0.178 3916 Planarity : 0.003 0.036 4499 Dihedral : 8.981 59.439 3982 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.29 % Allowed : 18.32 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.16), residues: 3146 helix: 0.79 (0.11), residues: 2431 sheet: None (None), residues: 0 loop : -1.41 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.014 0.001 TYR C 98 PHE 0.013 0.001 PHE D 214 TRP 0.009 0.001 TRP E 60 HIS 0.001 0.000 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (27302) covalent geometry : angle 0.49902 / 0.26 (36773) SS BOND : bond 0.00269 / 0.17 ( 33) SS BOND : angle 0.97036 / 0.70 ( 66) hydrogen bonds : bond 0.05387 / 3.42 ( 1364) hydrogen bonds : angle 3.02468 / 2.06 ( 3993) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 370 time to evaluate : 0.941 Fit side-chains REVERT: A 12 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.6985 (mm) REVERT: A 95 ARG cc_start: 0.7163 (ttt90) cc_final: 0.6785 (ttt90) REVERT: A 200 TYR cc_start: 0.8454 (t80) cc_final: 0.8209 (t80) REVERT: B 12 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7189 (mm) REVERT: B 30 SER cc_start: 0.8330 (t) cc_final: 0.8054 (p) REVERT: C 12 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7154 (mm) REVERT: C 169 GLU cc_start: 0.8113 (tp30) cc_final: 0.7194 (tp30) REVERT: C 276 GLN cc_start: 0.8236 (pt0) cc_final: 0.7737 (mt0) REVERT: D 12 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7178 (mm) REVERT: D 30 SER cc_start: 0.8101 (t) cc_final: 0.7829 (p) REVERT: E 12 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7316 (mm) REVERT: E 169 GLU cc_start: 0.8359 (tp30) cc_final: 0.7549 (tm-30) REVERT: F 12 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7321 (mm) REVERT: F 169 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7455 (tp30) REVERT: F 276 GLN cc_start: 0.8176 (pt0) cc_final: 0.7764 (mt0) REVERT: G 147 LYS cc_start: 0.7602 (tptt) cc_final: 0.7365 (OUTLIER) REVERT: G 169 GLU cc_start: 0.7949 (tp30) cc_final: 0.7411 (tm-30) REVERT: G 220 GLN cc_start: 0.8391 (tp40) cc_final: 0.8086 (tm-30) REVERT: H 12 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7308 (mm) REVERT: H 23 MET cc_start: 0.8193 (ttp) cc_final: 0.7796 (ttp) REVERT: H 25 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7444 (mt) REVERT: H 30 SER cc_start: 0.8221 (t) cc_final: 0.8005 (p) REVERT: H 95 ARG cc_start: 0.6845 (ttt90) cc_final: 0.6247 (ttt90) REVERT: H 169 GLU cc_start: 0.7831 (tp30) cc_final: 0.7370 (tp30) REVERT: H 276 GLN cc_start: 0.8200 (pt0) cc_final: 0.7903 (mt0) REVERT: I 12 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7167 (mm) REVERT: I 25 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7507 (mt) REVERT: I 30 SER cc_start: 0.8434 (t) cc_final: 0.8183 (p) REVERT: I 97 PHE cc_start: 0.8401 (m-80) cc_final: 0.8122 (m-80) REVERT: I 149 CYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6421 (t) REVERT: I 163 MET cc_start: 0.7608 (ttp) cc_final: 0.7363 (ttm) REVERT: I 169 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7424 (tp30) REVERT: I 249 LYS cc_start: 0.7881 (mttt) cc_final: 0.7553 (mtmm) REVERT: J 12 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7090 (mm) REVERT: J 72 ARG cc_start: 0.8620 (ttm170) cc_final: 0.8340 (ttp80) REVERT: J 169 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7491 (tp30) REVERT: J 220 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8140 (tp40) REVERT: J 276 GLN cc_start: 0.7946 (pt0) cc_final: 0.7586 (mt0) REVERT: J 283 ARG cc_start: 0.8792 (ttp80) cc_final: 0.8507 (ttp-170) REVERT: K 12 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7196 (mm) REVERT: K 25 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7457 (mt) REVERT: K 30 SER cc_start: 0.8382 (t) cc_final: 0.8072 (p) REVERT: K 129 MET cc_start: 0.8823 (tpp) cc_final: 0.8560 (mmt) REVERT: K 169 GLU cc_start: 0.8192 (tp30) cc_final: 0.7337 (tm-30) REVERT: K 276 GLN cc_start: 0.8312 (pt0) cc_final: 0.7914 (mt0) outliers start: 92 outliers final: 60 residues processed: 426 average time/residue: 0.6023 time to fit residues: 295.3032 Evaluate side-chains 438 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 365 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 94 CYS Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain K residue 231 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 204 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 194 optimal weight: 0.0270 chunk 201 optimal weight: 0.9980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN A 273 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN D 273 GLN E 176 GLN E 276 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN F 273 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 273 GLN H 102 GLN H 273 GLN I 273 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 273 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.159196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116388 restraints weight = 28174.654| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.89 r_work: 0.3183 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27335 Z= 0.103 Angle : 0.492 9.192 36839 Z= 0.251 Chirality : 0.036 0.177 3916 Planarity : 0.003 0.035 4499 Dihedral : 8.751 58.712 3982 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.90 % Allowed : 18.97 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.16), residues: 3146 helix: 0.95 (0.11), residues: 2431 sheet: None (None), residues: 0 loop : -1.36 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.019 0.001 TYR K 98 PHE 0.013 0.001 PHE D 88 TRP 0.010 0.001 TRP E 60 HIS 0.002 0.000 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (27302) covalent geometry : angle 0.49129 / 0.25 (36773) SS BOND : bond 0.00209 / 0.13 ( 33) SS BOND : angle 0.90510 / 0.64 ( 66) hydrogen bonds : bond 0.04989 / 3.17 ( 1364) hydrogen bonds : angle 2.98312 / 2.03 ( 3993) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 376 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6981 (mm) REVERT: A 22 PHE cc_start: 0.8082 (t80) cc_final: 0.7839 (t80) REVERT: A 30 SER cc_start: 0.8470 (t) cc_final: 0.8137 (p) REVERT: A 95 ARG cc_start: 0.7136 (ttt90) cc_final: 0.6792 (ttt90) REVERT: A 200 TYR cc_start: 0.8408 (t80) cc_final: 0.8160 (t80) REVERT: B 12 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7170 (mm) REVERT: B 30 SER cc_start: 0.8355 (t) cc_final: 0.8084 (p) REVERT: C 12 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7119 (mm) REVERT: C 169 GLU cc_start: 0.8139 (tp30) cc_final: 0.7169 (tp30) REVERT: C 276 GLN cc_start: 0.8195 (pt0) cc_final: 0.7715 (mt0) REVERT: C 283 ARG cc_start: 0.8911 (ttp80) cc_final: 0.8673 (ttp-170) REVERT: D 12 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7187 (mm) REVERT: D 30 SER cc_start: 0.8098 (t) cc_final: 0.7831 (p) REVERT: D 220 GLN cc_start: 0.8272 (tm-30) cc_final: 0.8047 (tp40) REVERT: E 12 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7315 (mm) REVERT: E 139 GLU cc_start: 0.6913 (pm20) cc_final: 0.6234 (mm-30) REVERT: E 169 GLU cc_start: 0.8291 (tp30) cc_final: 0.7527 (tm-30) REVERT: F 12 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7285 (mm) REVERT: F 169 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7443 (tp30) REVERT: F 276 GLN cc_start: 0.8161 (pt0) cc_final: 0.7746 (mt0) REVERT: G 147 LYS cc_start: 0.7609 (tptt) cc_final: 0.7379 (OUTLIER) REVERT: G 169 GLU cc_start: 0.7919 (tp30) cc_final: 0.7373 (tm-30) REVERT: H 12 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7307 (mm) REVERT: H 23 MET cc_start: 0.8136 (ttp) cc_final: 0.7723 (ttp) REVERT: H 25 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7456 (mt) REVERT: H 30 SER cc_start: 0.8235 (t) cc_final: 0.8025 (p) REVERT: H 95 ARG cc_start: 0.6828 (ttt90) cc_final: 0.6240 (ttt90) REVERT: H 169 GLU cc_start: 0.7816 (tp30) cc_final: 0.7347 (tp30) REVERT: H 276 GLN cc_start: 0.8174 (pt0) cc_final: 0.7867 (mt0) REVERT: I 12 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7175 (mm) REVERT: I 25 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7459 (mt) REVERT: I 30 SER cc_start: 0.8429 (t) cc_final: 0.8180 (p) REVERT: I 97 PHE cc_start: 0.8399 (m-80) cc_final: 0.8124 (m-80) REVERT: I 149 CYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6399 (t) REVERT: I 163 MET cc_start: 0.7613 (ttp) cc_final: 0.7391 (ttm) REVERT: I 169 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7420 (tp30) REVERT: I 249 LYS cc_start: 0.7822 (mttt) cc_final: 0.7488 (mtmm) REVERT: I 283 ARG cc_start: 0.8827 (ttp80) cc_final: 0.8527 (ttp-170) REVERT: J 12 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7063 (mm) REVERT: J 169 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7480 (tp30) REVERT: J 220 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8133 (tp40) REVERT: J 276 GLN cc_start: 0.7942 (pt0) cc_final: 0.7587 (mt0) REVERT: J 283 ARG cc_start: 0.8790 (ttp80) cc_final: 0.8511 (ttp-170) REVERT: K 12 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7271 (mm) REVERT: K 25 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7448 (mt) REVERT: K 30 SER cc_start: 0.8353 (t) cc_final: 0.8043 (p) REVERT: K 129 MET cc_start: 0.8794 (tpp) cc_final: 0.8568 (mmt) REVERT: K 169 GLU cc_start: 0.8150 (tp30) cc_final: 0.7271 (tm-30) REVERT: K 276 GLN cc_start: 0.8318 (pt0) cc_final: 0.7943 (mt0) outliers start: 81 outliers final: 54 residues processed: 426 average time/residue: 0.6490 time to fit residues: 317.2035 Evaluate side-chains 432 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 365 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 94 CYS Chi-restraints excluded: chain K residue 231 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 204 optimal weight: 4.9990 chunk 230 optimal weight: 0.0970 chunk 114 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 255 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN A 168 ASN A 273 GLN B 273 GLN D 273 GLN E 176 GLN E 273 GLN E 276 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN F 273 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 GLN H 102 GLN H 273 GLN I 102 GLN I 273 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 273 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.158826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116067 restraints weight = 28086.203| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.89 r_work: 0.3171 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27335 Z= 0.105 Angle : 0.504 12.127 36839 Z= 0.255 Chirality : 0.037 0.177 3916 Planarity : 0.003 0.034 4499 Dihedral : 8.527 59.614 3982 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.93 % Allowed : 19.04 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.16), residues: 3146 helix: 1.05 (0.11), residues: 2431 sheet: None (None), residues: 0 loop : -1.31 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.019 0.001 TYR E 98 PHE 0.014 0.001 PHE A 214 TRP 0.010 0.001 TRP E 60 HIS 0.003 0.000 HIS C 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (27302) covalent geometry : angle 0.50267 / 0.25 (36773) SS BOND : bond 0.00231 / 0.15 ( 33) SS BOND : angle 0.94923 / 0.68 ( 66) hydrogen bonds : bond 0.05105 / 3.24 ( 1364) hydrogen bonds : angle 2.97924 / 2.03 ( 3993) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 376 time to evaluate : 0.995 Fit side-chains REVERT: A 12 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7046 (mm) REVERT: A 95 ARG cc_start: 0.7088 (ttt90) cc_final: 0.6732 (ttt90) REVERT: A 200 TYR cc_start: 0.8413 (t80) cc_final: 0.8156 (t80) REVERT: B 12 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7179 (mm) REVERT: B 30 SER cc_start: 0.8352 (t) cc_final: 0.8080 (p) REVERT: C 12 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7116 (mm) REVERT: C 147 LYS cc_start: 0.7283 (ttpp) cc_final: 0.7038 (ptmm) REVERT: C 169 GLU cc_start: 0.8078 (tp30) cc_final: 0.7130 (tp30) REVERT: C 276 GLN cc_start: 0.8189 (pt0) cc_final: 0.7719 (mt0) REVERT: C 283 ARG cc_start: 0.8917 (ttp80) cc_final: 0.8679 (ttp-170) REVERT: D 12 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7124 (mm) REVERT: D 30 SER cc_start: 0.8096 (t) cc_final: 0.7829 (p) REVERT: D 220 GLN cc_start: 0.8277 (tm-30) cc_final: 0.8053 (tp40) REVERT: E 12 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7319 (mm) REVERT: E 169 GLU cc_start: 0.8275 (tp30) cc_final: 0.7504 (tm-30) REVERT: F 12 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7271 (mm) REVERT: F 169 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7411 (tp30) REVERT: F 276 GLN cc_start: 0.8154 (pt0) cc_final: 0.7737 (mt0) REVERT: G 147 LYS cc_start: 0.7557 (tptt) cc_final: 0.7351 (OUTLIER) REVERT: G 169 GLU cc_start: 0.7918 (tp30) cc_final: 0.7373 (tm-30) REVERT: G 220 GLN cc_start: 0.8293 (tp40) cc_final: 0.8041 (tm-30) REVERT: H 12 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7286 (mm) REVERT: H 23 MET cc_start: 0.8167 (ttp) cc_final: 0.7798 (ttp) REVERT: H 25 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7489 (mt) REVERT: H 30 SER cc_start: 0.8254 (t) cc_final: 0.7995 (p) REVERT: H 95 ARG cc_start: 0.6831 (ttt90) cc_final: 0.6233 (ttt90) REVERT: H 169 GLU cc_start: 0.7819 (tp30) cc_final: 0.7342 (tp30) REVERT: H 276 GLN cc_start: 0.8156 (pt0) cc_final: 0.7803 (mt0) REVERT: I 12 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7172 (mm) REVERT: I 25 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7459 (mt) REVERT: I 30 SER cc_start: 0.8439 (t) cc_final: 0.8191 (p) REVERT: I 97 PHE cc_start: 0.8367 (m-80) cc_final: 0.8093 (m-80) REVERT: I 149 CYS cc_start: 0.6704 (OUTLIER) cc_final: 0.6409 (t) REVERT: I 169 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7430 (tp30) REVERT: I 249 LYS cc_start: 0.7816 (mttt) cc_final: 0.7479 (mtmm) REVERT: I 283 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8528 (ttp-170) REVERT: J 12 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7034 (mm) REVERT: J 169 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7462 (tp30) REVERT: J 220 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8129 (tp40) REVERT: J 276 GLN cc_start: 0.7948 (pt0) cc_final: 0.7597 (mt0) REVERT: K 12 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7266 (mm) REVERT: K 25 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7462 (mt) REVERT: K 30 SER cc_start: 0.8353 (t) cc_final: 0.8026 (p) REVERT: K 129 MET cc_start: 0.8806 (tpp) cc_final: 0.8576 (mmt) REVERT: K 169 GLU cc_start: 0.8117 (tp30) cc_final: 0.7215 (tm-30) REVERT: K 276 GLN cc_start: 0.8291 (pt0) cc_final: 0.7935 (mt0) outliers start: 82 outliers final: 59 residues processed: 427 average time/residue: 0.6740 time to fit residues: 330.4154 Evaluate side-chains 443 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 371 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 142 CYS Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 94 CYS Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain K residue 231 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 203 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 260 optimal weight: 0.6980 chunk 100 optimal weight: 0.0980 chunk 229 optimal weight: 0.8980 chunk 267 optimal weight: 0.9990 chunk 261 optimal weight: 0.0010 chunk 124 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN A 273 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN E 176 GLN E 276 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN F 273 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 168 ASN H 273 GLN I 102 GLN I 273 GLN I 275 GLN J 176 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.161098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118565 restraints weight = 28046.408| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.89 r_work: 0.3212 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27335 Z= 0.091 Angle : 0.482 10.878 36839 Z= 0.244 Chirality : 0.035 0.177 3916 Planarity : 0.003 0.034 4499 Dihedral : 8.184 59.854 3982 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.43 % Allowed : 19.79 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.16), residues: 3146 helix: 1.25 (0.11), residues: 2431 sheet: None (None), residues: 0 loop : -1.24 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.020 0.001 TYR K 98 PHE 0.014 0.001 PHE D 88 TRP 0.010 0.001 TRP E 60 HIS 0.002 0.000 HIS D 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.09 (27302) covalent geometry : angle 0.48134 / 0.24 (36773) SS BOND : bond 0.00162 / 0.10 ( 33) SS BOND : angle 0.75725 / 0.54 ( 66) hydrogen bonds : bond 0.04239 / 2.68 ( 1364) hydrogen bonds : angle 2.89963 / 1.98 ( 3993) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 370 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7040 (mm) REVERT: A 26 LEU cc_start: 0.8268 (mt) cc_final: 0.8012 (OUTLIER) REVERT: A 30 SER cc_start: 0.8483 (t) cc_final: 0.8166 (p) REVERT: A 200 TYR cc_start: 0.8375 (t80) cc_final: 0.8109 (t80) REVERT: B 12 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7104 (mm) REVERT: B 30 SER cc_start: 0.8355 (t) cc_final: 0.8075 (p) REVERT: C 169 GLU cc_start: 0.8033 (tp30) cc_final: 0.7084 (tp30) REVERT: C 276 GLN cc_start: 0.8165 (pt0) cc_final: 0.7645 (mt0) REVERT: C 283 ARG cc_start: 0.8864 (ttp80) cc_final: 0.8613 (ttp-170) REVERT: D 12 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7080 (mm) REVERT: D 30 SER cc_start: 0.8120 (t) cc_final: 0.7851 (p) REVERT: D 169 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7284 (tp30) REVERT: D 220 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7943 (tp40) REVERT: E 12 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7266 (mm) REVERT: E 72 ARG cc_start: 0.8356 (ttp80) cc_final: 0.8120 (mtp180) REVERT: E 139 GLU cc_start: 0.6928 (pm20) cc_final: 0.6137 (mm-30) REVERT: E 169 GLU cc_start: 0.8205 (tp30) cc_final: 0.7207 (tp30) REVERT: F 12 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7228 (mm) REVERT: F 169 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7364 (tp30) REVERT: F 276 GLN cc_start: 0.8143 (pt0) cc_final: 0.7743 (mt0) REVERT: G 169 GLU cc_start: 0.7854 (tp30) cc_final: 0.7023 (OUTLIER) REVERT: H 12 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7262 (mm) REVERT: H 23 MET cc_start: 0.8076 (ttp) cc_final: 0.7712 (ttp) REVERT: H 25 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7478 (mt) REVERT: H 30 SER cc_start: 0.8236 (t) cc_final: 0.8029 (p) REVERT: H 95 ARG cc_start: 0.6744 (ttt90) cc_final: 0.6169 (ttt90) REVERT: H 169 GLU cc_start: 0.7707 (tp30) cc_final: 0.7234 (tp30) REVERT: H 276 GLN cc_start: 0.8065 (pt0) cc_final: 0.7714 (mt0) REVERT: I 12 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7141 (mm) REVERT: I 25 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7439 (mt) REVERT: I 30 SER cc_start: 0.8379 (t) cc_final: 0.8119 (p) REVERT: I 149 CYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6510 (t) REVERT: I 169 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7338 (tp30) REVERT: I 249 LYS cc_start: 0.7733 (mttt) cc_final: 0.7394 (mtmm) REVERT: J 12 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7019 (mm) REVERT: J 169 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7439 (tp30) REVERT: J 220 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8042 (tp40) REVERT: J 276 GLN cc_start: 0.7907 (pt0) cc_final: 0.7578 (mt0) REVERT: K 25 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7462 (mt) REVERT: K 30 SER cc_start: 0.8314 (t) cc_final: 0.8058 (p) REVERT: K 169 GLU cc_start: 0.8055 (tp30) cc_final: 0.7168 (tm-30) REVERT: K 276 GLN cc_start: 0.8251 (pt0) cc_final: 0.7882 (mt0) outliers start: 68 outliers final: 42 residues processed: 414 average time/residue: 0.6325 time to fit residues: 301.9969 Evaluate side-chains 408 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 356 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 142 CYS Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 94 CYS Chi-restraints excluded: chain K residue 231 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 192 optimal weight: 0.8980 chunk 306 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 209 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 71 optimal weight: 0.0170 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN A 273 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN D 273 GLN E 176 GLN E 276 GLN F 176 GLN F 273 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 273 GLN I 102 GLN I 273 GLN I 275 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 273 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116003 restraints weight = 26953.995| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.92 r_work: 0.3149 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27335 Z= 0.103 Angle : 0.504 11.557 36839 Z= 0.255 Chirality : 0.037 0.179 3916 Planarity : 0.003 0.049 4499 Dihedral : 8.173 59.958 3982 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.61 % Allowed : 19.90 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.16), residues: 3146 helix: 1.29 (0.11), residues: 2431 sheet: None (None), residues: 0 loop : -1.21 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.024 0.001 TYR E 98 PHE 0.012 0.001 PHE D 214 TRP 0.009 0.001 TRP E 60 HIS 0.003 0.000 HIS E 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (27302) covalent geometry : angle 0.50300 / 0.25 (36773) SS BOND : bond 0.00213 / 0.13 ( 33) SS BOND : angle 0.91106 / 0.64 ( 66) hydrogen bonds : bond 0.04876 / 3.09 ( 1364) hydrogen bonds : angle 2.92592 / 1.99 ( 3993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10163.73 seconds wall clock time: 186 minutes 50.61 seconds (11210.61 seconds total)