Starting phenix.real_space_refine on Tue Mar 3 17:29:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c9c_30311/03_2026/7c9c_30311.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c9c_30311/03_2026/7c9c_30311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c9c_30311/03_2026/7c9c_30311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c9c_30311/03_2026/7c9c_30311.map" model { file = "/net/cci-nas-00/data/ceres_data/7c9c_30311/03_2026/7c9c_30311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c9c_30311/03_2026/7c9c_30311.cif" } resolution = 3.33 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 18 5.49 5 S 33 5.16 5 C 4656 2.51 5 N 1293 2.21 5 O 1449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7452 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2392 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2392 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2392 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.65, per 1000 atoms: 0.22 Number of scatterers: 7452 At special positions: 0 Unit cell: (72.24, 113.4, 112.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 33 16.00 P 18 15.00 O 1449 8.00 N 1293 7.00 C 4656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 252.0 milliseconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1686 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 12 sheets defined 46.5% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 removed outlier: 4.096A pdb=" N LEU A 26 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 27 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 28 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS A 29 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A 31 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 42 removed outlier: 3.730A pdb=" N LYS A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.861A pdb=" N ILE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 47 through 52' Processing helix chain 'A' and resid 56 through 64 removed outlier: 4.242A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.713A pdb=" N GLU A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 97 removed outlier: 4.059A pdb=" N MET A 97 " --> pdb=" O LYS A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 97' Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.574A pdb=" N ASP A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 143 removed outlier: 3.609A pdb=" N CYS A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.829A pdb=" N GLY A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 175 removed outlier: 4.020A pdb=" N ASP A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 186 removed outlier: 3.722A pdb=" N VAL A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 213 removed outlier: 4.152A pdb=" N LEU A 203 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP A 204 " --> pdb=" O MET A 200 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.680A pdb=" N PHE A 233 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 260 removed outlier: 3.571A pdb=" N ALA A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.504A pdb=" N ALA A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 31 removed outlier: 4.094A pdb=" N LEU B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 27 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 28 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 29 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 31 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.730A pdb=" N LYS B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.860A pdb=" N ILE B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 52' Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.711A pdb=" N GLU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 97 removed outlier: 4.059A pdb=" N MET B 97 " --> pdb=" O LYS B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 97' Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.574A pdb=" N ASP B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 143 removed outlier: 3.609A pdb=" N CYS B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.828A pdb=" N GLY B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 removed outlier: 4.020A pdb=" N ASP B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 186 removed outlier: 3.722A pdb=" N VAL B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 213 removed outlier: 4.153A pdb=" N LEU B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP B 204 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.679A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 260 removed outlier: 3.570A pdb=" N ALA B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 252 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 removed outlier: 3.504A pdb=" N ALA B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 31 removed outlier: 4.094A pdb=" N LEU C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 27 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 28 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS C 29 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 31 " --> pdb=" O GLN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.730A pdb=" N LYS C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.860A pdb=" N ILE C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 52 " --> pdb=" O ILE C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 52' Processing helix chain 'C' and resid 56 through 64 removed outlier: 4.242A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 77 Processing helix chain 'C' and resid 88 through 93 removed outlier: 3.714A pdb=" N GLU C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 removed outlier: 4.059A pdb=" N MET C 97 " --> pdb=" O LYS C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 97' Processing helix chain 'C' and resid 105 through 113 removed outlier: 3.575A pdb=" N ASP C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 143 removed outlier: 3.608A pdb=" N CYS C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.828A pdb=" N GLY C 150 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 175 removed outlier: 4.020A pdb=" N ASP C 172 " --> pdb=" O ASP C 168 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 removed outlier: 3.721A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 213 removed outlier: 4.152A pdb=" N LEU C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP C 204 " --> pdb=" O MET C 200 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 removed outlier: 3.681A pdb=" N PHE C 233 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 260 removed outlier: 3.570A pdb=" N ALA C 247 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 297 removed outlier: 3.504A pdb=" N ALA C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA2, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.521A pdb=" N ALA A 313 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 268 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 126 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 267 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LYS A 155 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE A 221 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE A 157 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 156 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ALA A 191 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A 158 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 272 Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 331 removed outlier: 3.546A pdb=" N GLY A 334 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.520A pdb=" N ALA B 313 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 268 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 126 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 267 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS B 155 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE B 221 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE B 157 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA B 191 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE B 158 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 270 through 272 Processing sheet with id=AA8, first strand: chain 'B' and resid 330 through 331 removed outlier: 3.545A pdb=" N GLY B 334 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AB1, first strand: chain 'C' and resid 188 through 192 removed outlier: 6.629A pdb=" N ILE C 156 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA C 191 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE C 158 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LYS C 155 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE C 221 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE C 157 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 267 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN C 268 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 126 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 313 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AB3, first strand: chain 'C' and resid 330 through 331 removed outlier: 3.547A pdb=" N GLY C 334 " --> pdb=" O THR C 331 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 600 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: 1.00 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1654 1.33 - 1.45: 1544 1.45 - 1.57: 4302 1.57 - 1.69: 26 1.69 - 1.81: 57 Bond restraints: 7583 Sorted by residual: bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.544 0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.544 0.156 2.00e-02 2.50e+03 6.08e+01 bond pdb=" O3A ANP C 402 " pdb=" PB ANP C 402 " ideal model delta sigma weight residual 1.700 1.545 0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 1.795 1.682 0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 1.795 1.682 0.113 2.00e-02 2.50e+03 3.20e+01 ... (remaining 7578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 10152 3.84 - 7.68: 83 7.68 - 11.52: 12 11.52 - 15.36: 0 15.36 - 19.20: 3 Bond angle restraints: 10250 Sorted by residual: angle pdb=" PB ANP C 402 " pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 126.95 107.75 19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" PB ANP A 402 " pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 126.95 107.76 19.19 3.00e+00 1.11e-01 4.09e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 107.77 19.18 3.00e+00 1.11e-01 4.09e+01 angle pdb=" C LYS A 79 " pdb=" N LEU A 80 " pdb=" CA LEU A 80 " ideal model delta sigma weight residual 121.54 128.60 -7.06 1.91e+00 2.74e-01 1.37e+01 angle pdb=" C LYS B 79 " pdb=" N LEU B 80 " pdb=" CA LEU B 80 " ideal model delta sigma weight residual 121.54 128.57 -7.03 1.91e+00 2.74e-01 1.35e+01 ... (remaining 10245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.10: 4251 26.10 - 52.20: 270 52.20 - 78.30: 72 78.30 - 104.40: 21 104.40 - 130.50: 3 Dihedral angle restraints: 4617 sinusoidal: 1992 harmonic: 2625 Sorted by residual: dihedral pdb=" CA GLU A 82 " pdb=" C GLU A 82 " pdb=" N PRO A 83 " pdb=" CA PRO A 83 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA GLU C 82 " pdb=" C GLU C 82 " pdb=" N PRO C 83 " pdb=" CA PRO C 83 " ideal model delta harmonic sigma weight residual 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA GLU B 82 " pdb=" C GLU B 82 " pdb=" N PRO B 83 " pdb=" CA PRO B 83 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 4614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 914 0.062 - 0.124: 209 0.124 - 0.186: 25 0.186 - 0.248: 4 0.248 - 0.310: 3 Chirality restraints: 1155 Sorted by residual: chirality pdb=" C3' ANP A 402 " pdb=" C2' ANP A 402 " pdb=" C4' ANP A 402 " pdb=" O3' ANP A 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C3' ANP C 402 " pdb=" C2' ANP C 402 " pdb=" C4' ANP C 402 " pdb=" O3' ANP C 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1152 not shown) Planarity restraints: 1278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 128 " -0.009 2.00e-02 2.50e+03 1.51e-02 4.00e+00 pdb=" CG PHE B 128 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 128 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 128 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 128 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 128 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 128 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 128 " -0.009 2.00e-02 2.50e+03 1.51e-02 4.00e+00 pdb=" CG PHE C 128 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE C 128 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE C 128 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 128 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 128 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 128 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 128 " 0.008 2.00e-02 2.50e+03 1.49e-02 3.88e+00 pdb=" CG PHE A 128 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 128 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 128 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 128 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 128 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 128 " -0.001 2.00e-02 2.50e+03 ... (remaining 1275 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.97: 4 1.97 - 2.70: 235 2.70 - 3.43: 9286 3.43 - 4.17: 16840 4.17 - 4.90: 31357 Nonbonded interactions: 57722 Sorted by model distance: nonbonded pdb=" NH1 ARG C 56 " pdb=" OD1 ASP C 71 " model vdw 1.232 3.120 nonbonded pdb="CA CA B 401 " pdb=" O1G ANP B 402 " model vdw 1.678 2.510 nonbonded pdb="CA CA C 401 " pdb=" O1G ANP C 402 " model vdw 1.763 2.510 nonbonded pdb=" CZ ARG C 56 " pdb=" OD1 ASP C 71 " model vdw 1.789 3.270 nonbonded pdb="CA CA A 401 " pdb=" O1G ANP A 402 " model vdw 1.989 2.510 ... (remaining 57717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 5.200 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.620 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 0.156 7586 Z= 0.398 Angle : 1.035 19.200 10250 Z= 0.529 Chirality : 0.056 0.310 1155 Planarity : 0.005 0.041 1278 Dihedral : 19.223 130.497 2931 Min Nonbonded Distance : 1.232 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.79 % Allowed : 6.98 % Favored : 92.23 % 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: -5.45 (0.20), residues: 912 helix: -5.12 (0.06), residues: 351 sheet: -1.95 (0.38), residues: 156 loop : -2.68 (0.24), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 57 TYR 0.014 0.002 TYR A 316 PHE 0.033 0.003 PHE C 128 HIS 0.009 0.002 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00854 ( 7583) covalent geometry : angle 1.03488 (10250) hydrogen bonds : bond 0.30424 ( 217) hydrogen bonds : angle 9.83353 ( 600) Misc. bond : bond 0.02966 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.7771 (p0) cc_final: 0.7493 (m-30) REVERT: A 252 ARG cc_start: 0.8046 (tpt-90) cc_final: 0.7747 (ttt90) REVERT: B 41 LYS cc_start: 0.6961 (mttt) cc_final: 0.6394 (mttm) REVERT: B 171 ARG cc_start: 0.7424 (tpt170) cc_final: 0.7139 (mtt90) REVERT: C 36 ASP cc_start: 0.6220 (m-30) cc_final: 0.6009 (m-30) REVERT: C 41 LYS cc_start: 0.6410 (mttt) cc_final: 0.5726 (tptt) REVERT: C 285 LYS cc_start: 0.8990 (mttt) cc_final: 0.8372 (mmmt) outliers start: 6 outliers final: 3 residues processed: 177 average time/residue: 0.1271 time to fit residues: 27.6544 Evaluate side-chains 116 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 22 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 78 ASN A 199 GLN A 248 GLN B 61 ASN B 78 ASN B 198 HIS B 199 GLN B 295 HIS C 61 ASN C 78 ASN C 187 ASN C 198 HIS C 199 GLN C 248 GLN C 295 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.133728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.099316 restraints weight = 9092.139| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.89 r_work: 0.2787 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7586 Z= 0.134 Angle : 0.551 7.165 10250 Z= 0.286 Chirality : 0.042 0.135 1155 Planarity : 0.005 0.073 1278 Dihedral : 15.644 153.243 1184 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.19 % Allowed : 12.91 % Favored : 85.90 % 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: -4.48 (0.23), residues: 912 helix: -3.85 (0.15), residues: 390 sheet: -1.92 (0.37), residues: 189 loop : -2.09 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 169 TYR 0.005 0.001 TYR C 316 PHE 0.020 0.001 PHE A 128 HIS 0.003 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7583) covalent geometry : angle 0.55136 (10250) hydrogen bonds : bond 0.03513 ( 217) hydrogen bonds : angle 4.89119 ( 600) Misc. bond : bond 0.00162 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 168 ASP cc_start: 0.8377 (p0) cc_final: 0.7895 (m-30) REVERT: B 41 LYS cc_start: 0.6529 (mttt) cc_final: 0.5795 (mttm) REVERT: B 168 ASP cc_start: 0.8398 (p0) cc_final: 0.7652 (m-30) REVERT: B 171 ARG cc_start: 0.6988 (tpt170) cc_final: 0.6295 (mtt-85) REVERT: B 325 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8625 (mt-10) REVERT: C 41 LYS cc_start: 0.6077 (mttt) cc_final: 0.5393 (tptt) REVERT: C 285 LYS cc_start: 0.9019 (mttt) cc_final: 0.7960 (mmmt) outliers start: 9 outliers final: 4 residues processed: 123 average time/residue: 0.1077 time to fit residues: 17.2489 Evaluate side-chains 103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 chunk 34 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.0570 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.131229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.097429 restraints weight = 9050.489| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.76 r_work: 0.2778 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7586 Z= 0.127 Angle : 0.502 6.911 10250 Z= 0.264 Chirality : 0.042 0.154 1155 Planarity : 0.005 0.117 1278 Dihedral : 14.661 158.927 1173 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.84 % Allowed : 13.04 % Favored : 85.11 % 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: -3.71 (0.25), residues: 912 helix: -2.89 (0.20), residues: 405 sheet: -1.61 (0.37), residues: 189 loop : -2.00 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 169 TYR 0.014 0.001 TYR B 316 PHE 0.016 0.001 PHE A 128 HIS 0.003 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7583) covalent geometry : angle 0.50199 (10250) hydrogen bonds : bond 0.03250 ( 217) hydrogen bonds : angle 4.22563 ( 600) Misc. bond : bond 0.00217 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.296 Fit side-chains REVERT: A 168 ASP cc_start: 0.8249 (p0) cc_final: 0.8019 (m-30) REVERT: A 241 GLU cc_start: 0.8541 (tt0) cc_final: 0.8293 (tt0) REVERT: B 41 LYS cc_start: 0.6613 (mttt) cc_final: 0.5861 (mttm) REVERT: B 186 ASP cc_start: 0.8336 (m-30) cc_final: 0.7712 (m-30) REVERT: B 325 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8616 (mt-10) REVERT: C 41 LYS cc_start: 0.6097 (mttt) cc_final: 0.5418 (tptt) REVERT: C 96 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8894 (mttp) REVERT: C 285 LYS cc_start: 0.9032 (mttt) cc_final: 0.7993 (mmmt) outliers start: 14 outliers final: 5 residues processed: 111 average time/residue: 0.1071 time to fit residues: 15.4562 Evaluate side-chains 103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 GLN C 291 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.131214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.095268 restraints weight = 9267.835| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.00 r_work: 0.2775 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7586 Z= 0.117 Angle : 0.483 6.295 10250 Z= 0.252 Chirality : 0.042 0.146 1155 Planarity : 0.007 0.156 1278 Dihedral : 14.645 160.173 1173 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.11 % Allowed : 12.78 % Favored : 85.11 % 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: -3.13 (0.26), residues: 912 helix: -2.30 (0.23), residues: 405 sheet: -1.46 (0.38), residues: 189 loop : -1.78 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 169 TYR 0.010 0.001 TYR B 316 PHE 0.015 0.001 PHE A 128 HIS 0.003 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7583) covalent geometry : angle 0.48314 (10250) hydrogen bonds : bond 0.02826 ( 217) hydrogen bonds : angle 3.93014 ( 600) Misc. bond : bond 0.00412 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.251 Fit side-chains REVERT: A 241 GLU cc_start: 0.8596 (tt0) cc_final: 0.8328 (tt0) REVERT: B 41 LYS cc_start: 0.6591 (mttt) cc_final: 0.5840 (mttm) REVERT: B 186 ASP cc_start: 0.8421 (m-30) cc_final: 0.8061 (m-30) REVERT: B 325 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8619 (mt-10) REVERT: C 36 ASP cc_start: 0.6929 (m-30) cc_final: 0.6705 (m-30) REVERT: C 41 LYS cc_start: 0.6071 (mttt) cc_final: 0.5390 (tptt) REVERT: C 93 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7962 (mm-30) REVERT: C 96 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8634 (mttp) REVERT: C 285 LYS cc_start: 0.9062 (mttt) cc_final: 0.8052 (mmmt) outliers start: 16 outliers final: 8 residues processed: 115 average time/residue: 0.0946 time to fit residues: 14.3331 Evaluate side-chains 105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 72 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 40 optimal weight: 0.0770 chunk 62 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.141856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.106626 restraints weight = 9037.961| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.00 r_work: 0.2822 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7586 Z= 0.074 Angle : 0.430 6.411 10250 Z= 0.225 Chirality : 0.040 0.135 1155 Planarity : 0.007 0.171 1278 Dihedral : 14.309 160.909 1173 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.92 % Allowed : 13.97 % Favored : 85.11 % 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: -2.65 (0.27), residues: 912 helix: -1.87 (0.24), residues: 408 sheet: -1.32 (0.37), residues: 189 loop : -1.52 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 169 TYR 0.004 0.001 TYR B 316 PHE 0.012 0.001 PHE A 128 HIS 0.002 0.000 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00163 ( 7583) covalent geometry : angle 0.43020 (10250) hydrogen bonds : bond 0.02027 ( 217) hydrogen bonds : angle 3.64853 ( 600) Misc. bond : bond 0.00297 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.276 Fit side-chains REVERT: A 241 GLU cc_start: 0.8580 (tt0) cc_final: 0.8322 (tt0) REVERT: B 41 LYS cc_start: 0.6556 (mttt) cc_final: 0.5818 (mttm) REVERT: B 80 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6812 (mm) REVERT: B 186 ASP cc_start: 0.8393 (m-30) cc_final: 0.7983 (m-30) REVERT: B 325 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8623 (mt-10) REVERT: C 36 ASP cc_start: 0.6885 (m-30) cc_final: 0.6643 (m-30) REVERT: C 41 LYS cc_start: 0.6015 (mttt) cc_final: 0.5341 (tptt) REVERT: C 93 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7844 (mm-30) REVERT: C 96 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8518 (mttp) REVERT: C 285 LYS cc_start: 0.9063 (mttt) cc_final: 0.8094 (mmmt) outliers start: 7 outliers final: 4 residues processed: 110 average time/residue: 0.1023 time to fit residues: 14.8642 Evaluate side-chains 105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 14 optimal weight: 0.1980 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 0.0470 chunk 33 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN C 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.129175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.094931 restraints weight = 9241.391| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.88 r_work: 0.2732 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7586 Z= 0.143 Angle : 0.491 6.264 10250 Z= 0.256 Chirality : 0.043 0.145 1155 Planarity : 0.006 0.141 1278 Dihedral : 14.740 164.749 1173 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.24 % Allowed : 13.44 % Favored : 84.32 % 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: -2.24 (0.27), residues: 912 helix: -1.35 (0.25), residues: 396 sheet: -1.21 (0.37), residues: 189 loop : -1.54 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 169 TYR 0.010 0.001 TYR B 316 PHE 0.012 0.001 PHE A 128 HIS 0.004 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7583) covalent geometry : angle 0.49073 (10250) hydrogen bonds : bond 0.03177 ( 217) hydrogen bonds : angle 3.83186 ( 600) Misc. bond : bond 0.00337 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 241 GLU cc_start: 0.8653 (tt0) cc_final: 0.8388 (tt0) REVERT: B 41 LYS cc_start: 0.6583 (mttt) cc_final: 0.5832 (mttm) REVERT: B 80 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6943 (mm) REVERT: B 273 ASP cc_start: 0.8649 (t0) cc_final: 0.8399 (t0) REVERT: B 325 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8613 (mt-10) REVERT: C 36 ASP cc_start: 0.7087 (m-30) cc_final: 0.6807 (m-30) REVERT: C 41 LYS cc_start: 0.6008 (mttt) cc_final: 0.5366 (tptt) REVERT: C 86 LEU cc_start: 0.8431 (mt) cc_final: 0.8191 (mt) REVERT: C 197 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8373 (mp0) REVERT: C 285 LYS cc_start: 0.9124 (mttt) cc_final: 0.8094 (mmmt) outliers start: 17 outliers final: 8 residues processed: 117 average time/residue: 0.1014 time to fit residues: 15.4041 Evaluate side-chains 107 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 GLN C 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.130711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.094480 restraints weight = 9250.751| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.07 r_work: 0.2754 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 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 0.019 7586 Z= 0.106 Angle : 0.458 6.051 10250 Z= 0.240 Chirality : 0.042 0.133 1155 Planarity : 0.008 0.182 1278 Dihedral : 14.740 168.800 1173 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.71 % Allowed : 13.97 % Favored : 84.32 % 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: -1.96 (0.27), residues: 912 helix: -1.11 (0.26), residues: 399 sheet: -1.05 (0.37), residues: 189 loop : -1.40 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 169 TYR 0.007 0.001 TYR B 316 PHE 0.013 0.001 PHE A 128 HIS 0.002 0.000 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7583) covalent geometry : angle 0.45835 (10250) hydrogen bonds : bond 0.02596 ( 217) hydrogen bonds : angle 3.66983 ( 600) Misc. bond : bond 0.00402 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 241 GLU cc_start: 0.8651 (tt0) cc_final: 0.8407 (tt0) REVERT: B 41 LYS cc_start: 0.6635 (mttt) cc_final: 0.5863 (mttm) REVERT: B 80 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6908 (mm) REVERT: B 273 ASP cc_start: 0.8615 (t0) cc_final: 0.8379 (t0) REVERT: B 325 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8592 (mt-10) REVERT: C 41 LYS cc_start: 0.6019 (mttt) cc_final: 0.5382 (tptt) REVERT: C 96 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8695 (mttp) REVERT: C 285 LYS cc_start: 0.9123 (mttt) cc_final: 0.8100 (mmmt) outliers start: 13 outliers final: 7 residues processed: 113 average time/residue: 0.0962 time to fit residues: 14.3096 Evaluate side-chains 109 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 57 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 56 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN C 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.127251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.098195 restraints weight = 9252.030| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.50 r_work: 0.2791 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7586 Z= 0.161 Angle : 0.509 5.723 10250 Z= 0.265 Chirality : 0.044 0.136 1155 Planarity : 0.008 0.180 1278 Dihedral : 14.888 179.257 1173 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.71 % Allowed : 14.62 % Favored : 83.66 % 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: -1.88 (0.28), residues: 912 helix: -1.02 (0.26), residues: 402 sheet: -1.00 (0.38), residues: 189 loop : -1.40 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 169 TYR 0.011 0.001 TYR C 316 PHE 0.013 0.002 PHE A 128 HIS 0.004 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 7583) covalent geometry : angle 0.50869 (10250) hydrogen bonds : bond 0.03347 ( 217) hydrogen bonds : angle 3.85667 ( 600) Misc. bond : bond 0.00416 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.309 Fit side-chains REVERT: B 41 LYS cc_start: 0.6863 (mttt) cc_final: 0.6045 (mttm) REVERT: B 80 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.7044 (mm) REVERT: B 186 ASP cc_start: 0.8433 (m-30) cc_final: 0.7960 (m-30) REVERT: B 325 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8537 (mt-10) REVERT: C 41 LYS cc_start: 0.6243 (mttt) cc_final: 0.5702 (tptt) REVERT: C 96 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8845 (mttp) REVERT: C 180 ASP cc_start: 0.8218 (m-30) cc_final: 0.7540 (t0) REVERT: C 201 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7409 (tt0) REVERT: C 285 LYS cc_start: 0.9225 (mttt) cc_final: 0.8300 (mmmt) outliers start: 13 outliers final: 9 residues processed: 116 average time/residue: 0.1085 time to fit residues: 16.1821 Evaluate side-chains 105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.127769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.092025 restraints weight = 9234.528| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.06 r_work: 0.2696 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7586 Z= 0.179 Angle : 0.533 5.772 10250 Z= 0.277 Chirality : 0.044 0.137 1155 Planarity : 0.013 0.319 1278 Dihedral : 15.057 176.916 1173 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.71 % Allowed : 14.49 % Favored : 83.79 % 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: -1.83 (0.28), residues: 912 helix: -1.04 (0.26), residues: 405 sheet: -0.79 (0.39), residues: 183 loop : -1.44 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG A 169 TYR 0.013 0.001 TYR C 316 PHE 0.015 0.002 PHE A 128 HIS 0.004 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 7583) covalent geometry : angle 0.53297 (10250) hydrogen bonds : bond 0.03372 ( 217) hydrogen bonds : angle 3.87821 ( 600) Misc. bond : bond 0.00679 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.278 Fit side-chains REVERT: B 41 LYS cc_start: 0.6732 (mttt) cc_final: 0.5933 (mttm) REVERT: B 80 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6972 (mm) REVERT: B 186 ASP cc_start: 0.8561 (m-30) cc_final: 0.8011 (m-30) REVERT: B 325 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8602 (mt-10) REVERT: C 41 LYS cc_start: 0.6195 (mttt) cc_final: 0.5646 (tptt) REVERT: C 201 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7263 (tt0) REVERT: C 285 LYS cc_start: 0.9181 (mttt) cc_final: 0.8107 (mmmt) outliers start: 13 outliers final: 10 residues processed: 106 average time/residue: 0.0887 time to fit residues: 12.5653 Evaluate side-chains 105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 18 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.0170 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 0.0470 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.132754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.096680 restraints weight = 9163.600| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.13 r_work: 0.2781 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7586 Z= 0.079 Angle : 0.440 6.114 10250 Z= 0.230 Chirality : 0.041 0.128 1155 Planarity : 0.010 0.285 1278 Dihedral : 14.327 172.523 1173 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.19 % Allowed : 15.55 % Favored : 83.27 % 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: -1.60 (0.28), residues: 912 helix: -0.74 (0.26), residues: 405 sheet: -1.06 (0.38), residues: 195 loop : -1.18 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 169 TYR 0.004 0.001 TYR C 316 PHE 0.013 0.001 PHE A 128 HIS 0.001 0.000 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00173 ( 7583) covalent geometry : angle 0.43983 (10250) hydrogen bonds : bond 0.02030 ( 217) hydrogen bonds : angle 3.56879 ( 600) Misc. bond : bond 0.00450 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.293 Fit side-chains REVERT: B 41 LYS cc_start: 0.6591 (mttt) cc_final: 0.5825 (mttm) REVERT: B 80 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6684 (mm) REVERT: B 86 LEU cc_start: 0.8390 (tp) cc_final: 0.8162 (mt) REVERT: B 168 ASP cc_start: 0.8392 (p0) cc_final: 0.8055 (p0) REVERT: B 186 ASP cc_start: 0.8534 (m-30) cc_final: 0.7874 (m-30) REVERT: B 325 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8613 (mt-10) REVERT: C 41 LYS cc_start: 0.6163 (mttt) cc_final: 0.5615 (tptt) REVERT: C 96 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8714 (mttp) REVERT: C 285 LYS cc_start: 0.9133 (mttt) cc_final: 0.8104 (mmmt) outliers start: 9 outliers final: 5 residues processed: 113 average time/residue: 0.1016 time to fit residues: 15.0563 Evaluate side-chains 106 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 18 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.132344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.098700 restraints weight = 9127.161| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.07 r_work: 0.2810 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7586 Z= 0.084 Angle : 0.437 5.566 10250 Z= 0.229 Chirality : 0.041 0.128 1155 Planarity : 0.010 0.268 1278 Dihedral : 14.217 177.528 1173 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.19 % Allowed : 15.94 % Favored : 82.87 % 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: -1.43 (0.28), residues: 912 helix: -0.61 (0.27), residues: 408 sheet: -0.86 (0.38), residues: 189 loop : -1.18 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 169 TYR 0.005 0.001 TYR C 316 PHE 0.011 0.001 PHE A 128 HIS 0.002 0.000 HIS C 295 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 7583) covalent geometry : angle 0.43657 (10250) hydrogen bonds : bond 0.02251 ( 217) hydrogen bonds : angle 3.54012 ( 600) Misc. bond : bond 0.00446 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1968.45 seconds wall clock time: 34 minutes 16.66 seconds (2056.66 seconds total)