Starting phenix.real_space_refine on Fri Jun 13 11:04:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbo_27293/06_2025/8dbo_27293.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbo_27293/06_2025/8dbo_27293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbo_27293/06_2025/8dbo_27293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbo_27293/06_2025/8dbo_27293.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbo_27293/06_2025/8dbo_27293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbo_27293/06_2025/8dbo_27293.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.347 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 12 5.21 5 S 102 5.16 5 C 9210 2.51 5 N 2628 2.21 5 O 2898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14880 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2416 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 7.03, per 1000 atoms: 0.47 Number of scatterers: 14880 At special positions: 0 Unit cell: (120.35, 126.99, 75.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 30 15.00 Mg 12 11.99 O 2898 8.00 N 2628 7.00 C 9210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.92 Conformation dependent library (CDL) restraints added in 1.9 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 18 sheets defined 43.4% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 62 through 80 Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 226 through 239 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.708A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 62 through 80 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 226 through 239 Processing helix chain 'B' and resid 256 through 263 Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.708A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'C' and resid 12 through 23 Processing helix chain 'C' and resid 62 through 80 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 161 through 164 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 226 through 239 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.708A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 306 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 62 through 80 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 131 through 138 Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 161 through 164 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 174 through 186 Processing helix chain 'D' and resid 226 through 239 Processing helix chain 'D' and resid 256 through 263 Processing helix chain 'D' and resid 277 through 284 removed outlier: 3.708A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 306 Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'E' and resid 12 through 23 Processing helix chain 'E' and resid 62 through 80 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 131 through 138 Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 161 through 164 Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 174 through 186 Processing helix chain 'E' and resid 226 through 239 Processing helix chain 'E' and resid 256 through 263 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.708A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 306 Processing helix chain 'E' and resid 309 through 314 Processing helix chain 'F' and resid 12 through 23 Processing helix chain 'F' and resid 62 through 80 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 131 through 138 Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 161 through 164 Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 226 through 239 Processing helix chain 'F' and resid 256 through 263 Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.707A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 306 Processing helix chain 'F' and resid 309 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.121A pdb=" N LYS A 5 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL A 56 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE A 7 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A 88 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET A 127 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 124 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU A 145 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A 126 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 208 removed outlier: 6.117A pdb=" N ILE A 167 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 192 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER A 169 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS A 194 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 249 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET A 222 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY A 251 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A 244 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 272 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS A 250 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLN A 288 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 271 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.121A pdb=" N LYS B 5 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL B 56 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE B 7 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL B 88 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET B 127 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 124 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU B 145 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR B 126 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA6, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.117A pdb=" N ILE B 167 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE B 192 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER B 169 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS B 194 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 249 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N MET B 222 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY B 251 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 244 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 272 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS B 250 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLN B 288 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 269 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE B 290 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 271 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.121A pdb=" N LYS C 5 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL C 56 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE C 7 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET C 127 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 124 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU C 145 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR C 126 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AA9, first strand: chain 'C' and resid 205 through 208 removed outlier: 6.117A pdb=" N ILE C 167 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE C 192 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER C 169 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LYS C 194 " --> pdb=" O SER C 169 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR C 249 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET C 222 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY C 251 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C 244 " --> pdb=" O PHE C 266 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 272 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS C 250 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLN C 288 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL C 269 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE C 290 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL C 271 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.121A pdb=" N LYS D 5 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL D 56 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE D 7 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL D 88 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET D 127 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE D 124 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU D 145 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 208 removed outlier: 6.117A pdb=" N ILE D 167 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE D 192 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER D 169 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS D 194 " --> pdb=" O SER D 169 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR D 249 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET D 222 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY D 251 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL D 244 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR D 272 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N HIS D 250 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLN D 288 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE D 290 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 271 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.121A pdb=" N LYS E 5 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL E 56 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE E 7 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL E 88 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET E 127 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE E 124 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU E 145 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR E 126 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 34 Processing sheet with id=AB6, first strand: chain 'E' and resid 205 through 208 removed outlier: 6.117A pdb=" N ILE E 167 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE E 192 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER E 169 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS E 194 " --> pdb=" O SER E 169 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR E 249 " --> pdb=" O ASP E 220 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET E 222 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY E 251 " --> pdb=" O MET E 222 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL E 244 " --> pdb=" O PHE E 266 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR E 272 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS E 250 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLN E 288 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL E 269 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE E 290 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL E 271 " --> pdb=" O ILE E 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.121A pdb=" N LYS F 5 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL F 56 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE F 7 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL F 88 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET F 127 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE F 124 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU F 145 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR F 126 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 208 removed outlier: 6.117A pdb=" N ILE F 167 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE F 192 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER F 169 " --> pdb=" O ILE F 192 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS F 194 " --> pdb=" O SER F 169 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR F 249 " --> pdb=" O ASP F 220 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N MET F 222 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLY F 251 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL F 244 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR F 272 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS F 250 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLN F 288 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL F 269 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE F 290 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL F 271 " --> pdb=" O ILE F 290 " (cutoff:3.500A) 660 hydrogen bonds defined for protein. 1800 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: 4.92 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4953 1.34 - 1.46: 1956 1.46 - 1.57: 7989 1.57 - 1.69: 36 1.69 - 1.81: 150 Bond restraints: 15084 Sorted by residual: bond pdb=" C4 ADP A 405 " pdb=" C5 ADP A 405 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C4 ADP B 405 " pdb=" C5 ADP B 405 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 15079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 20094 2.97 - 5.94: 234 5.94 - 8.91: 100 8.91 - 11.88: 32 11.88 - 14.85: 12 Bond angle restraints: 20472 Sorted by residual: angle pdb=" PA ADP F 403 " pdb=" O3A ADP F 403 " pdb=" PB ADP F 403 " ideal model delta sigma weight residual 120.50 135.35 -14.85 3.00e+00 1.11e-01 2.45e+01 angle pdb=" PA ADP E 403 " pdb=" O3A ADP E 403 " pdb=" PB ADP E 403 " ideal model delta sigma weight residual 120.50 135.35 -14.85 3.00e+00 1.11e-01 2.45e+01 angle pdb=" PA ADP C 403 " pdb=" O3A ADP C 403 " pdb=" PB ADP C 403 " ideal model delta sigma weight residual 120.50 135.34 -14.84 3.00e+00 1.11e-01 2.45e+01 angle pdb=" PA ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sigma weight residual 120.50 135.32 -14.82 3.00e+00 1.11e-01 2.44e+01 angle pdb=" PA ADP D 402 " pdb=" O3A ADP D 402 " pdb=" PB ADP D 402 " ideal model delta sigma weight residual 120.50 135.31 -14.81 3.00e+00 1.11e-01 2.44e+01 ... (remaining 20467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 8826 34.00 - 67.99: 297 67.99 - 101.99: 33 101.99 - 135.99: 15 135.99 - 169.99: 9 Dihedral angle restraints: 9180 sinusoidal: 3672 harmonic: 5508 Sorted by residual: dihedral pdb=" O2A ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PA ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 109.99 -169.99 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP D 402 " pdb=" O3A ADP D 402 " pdb=" PA ADP D 402 " pdb=" PB ADP D 402 " ideal model delta sinusoidal sigma weight residual -60.00 109.97 -169.97 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP F 403 " pdb=" O3A ADP F 403 " pdb=" PA ADP F 403 " pdb=" PB ADP F 403 " ideal model delta sinusoidal sigma weight residual -60.00 109.95 -169.95 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 9177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1508 0.041 - 0.082: 600 0.082 - 0.123: 240 0.123 - 0.163: 46 0.163 - 0.204: 12 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CA VAL C 151 " pdb=" N VAL C 151 " pdb=" C VAL C 151 " pdb=" CB VAL C 151 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL B 151 " pdb=" N VAL B 151 " pdb=" C VAL B 151 " pdb=" CB VAL B 151 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL E 151 " pdb=" N VAL E 151 " pdb=" C VAL E 151 " pdb=" CB VAL E 151 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2403 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 65 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" CG ASP C 65 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP C 65 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP C 65 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP B 402 " 0.019 2.00e-02 2.50e+03 9.40e-03 2.43e+00 pdb=" C2 ADP B 402 " -0.005 2.00e-02 2.50e+03 pdb=" C4 ADP B 402 " -0.002 2.00e-02 2.50e+03 pdb=" C5 ADP B 402 " -0.003 2.00e-02 2.50e+03 pdb=" C6 ADP B 402 " -0.000 2.00e-02 2.50e+03 pdb=" C8 ADP B 402 " -0.009 2.00e-02 2.50e+03 pdb=" N1 ADP B 402 " -0.005 2.00e-02 2.50e+03 pdb=" N3 ADP B 402 " -0.003 2.00e-02 2.50e+03 pdb=" N6 ADP B 402 " 0.019 2.00e-02 2.50e+03 pdb=" N7 ADP B 402 " -0.009 2.00e-02 2.50e+03 pdb=" N9 ADP B 402 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 65 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" CG ASP A 65 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP A 65 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 65 " -0.010 2.00e-02 2.50e+03 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 96 2.47 - 3.08: 10623 3.08 - 3.69: 24138 3.69 - 4.29: 37203 4.29 - 4.90: 59181 Nonbonded interactions: 131241 Sorted by model distance: nonbonded pdb="MG MG B 403 " pdb=" O HOH B 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG F 404 " pdb=" O HOH F 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG A 403 " pdb=" O HOH A 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG E 404 " pdb=" O HOH E 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG D 403 " pdb=" O HOH D 503 " model vdw 1.867 2.170 ... (remaining 131236 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 317 or resid 404)) selection = (chain 'B' and (resid 2 through 317 or resid 404)) selection = (chain 'C' and (resid 2 through 317 or resid 404)) selection = (chain 'D' and (resid 2 through 317 or resid 404)) selection = (chain 'E' and (resid 2 through 317 or resid 404)) selection = (chain 'F' and (resid 2 through 317 or resid 404)) } 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: 2.970 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.240 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.040 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:14.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 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 : 0.007 0.107 15084 Z= 0.343 Angle : 1.022 14.848 20472 Z= 0.449 Chirality : 0.053 0.204 2406 Planarity : 0.003 0.020 2568 Dihedral : 18.642 169.985 5592 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.37 % Allowed : 14.23 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), residues: 1884 helix: 1.78 (0.20), residues: 702 sheet: -0.38 (0.24), residues: 450 loop : 0.24 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP E 162 HIS 0.007 0.001 HIS F 12 PHE 0.013 0.002 PHE F 138 TYR 0.011 0.002 TYR E 311 ARG 0.008 0.001 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.14915 ( 660) hydrogen bonds : angle 5.25072 ( 1800) covalent geometry : bond 0.00703 (15084) covalent geometry : angle 1.02227 (20472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 555 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.7724 (tt) cc_final: 0.7510 (mm) REVERT: A 280 LYS cc_start: 0.7820 (mmtm) cc_final: 0.7457 (mmmt) REVERT: B 280 LYS cc_start: 0.7870 (mmtm) cc_final: 0.7540 (mmmt) REVERT: C 191 LEU cc_start: 0.7852 (tt) cc_final: 0.7588 (mm) REVERT: C 280 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7680 (mmmt) REVERT: D 191 LEU cc_start: 0.7854 (tt) cc_final: 0.7601 (mm) REVERT: D 280 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7699 (mmmt) REVERT: E 280 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7544 (mmmt) REVERT: F 280 LYS cc_start: 0.7829 (mmtm) cc_final: 0.7463 (mmmt) outliers start: 54 outliers final: 11 residues processed: 591 average time/residue: 1.3573 time to fit residues: 875.4249 Evaluate side-chains 382 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 371 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 196 ARG Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.5980 chunk 140 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN B 263 ASN C 133 GLN C 283 HIS D 133 GLN D 283 HIS E 97 GLN E 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.272479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.258601 restraints weight = 13447.367| |-----------------------------------------------------------------------------| r_work (start): 0.4960 rms_B_bonded: 0.85 r_work: 0.4917 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.4836 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.4836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15084 Z= 0.135 Angle : 0.686 8.715 20472 Z= 0.319 Chirality : 0.048 0.156 2406 Planarity : 0.004 0.028 2568 Dihedral : 16.080 165.682 2170 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.37 % Allowed : 22.41 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 1884 helix: 1.43 (0.19), residues: 756 sheet: -0.77 (0.23), residues: 492 loop : -0.31 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 154 HIS 0.008 0.001 HIS C 12 PHE 0.011 0.002 PHE A 313 TYR 0.010 0.002 TYR E 311 ARG 0.004 0.001 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 660) hydrogen bonds : angle 4.55208 ( 1800) covalent geometry : bond 0.00290 (15084) covalent geometry : angle 0.68626 (20472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 351 time to evaluate : 1.605 Fit side-chains REVERT: A 78 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6762 (ttmt) REVERT: F 78 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6687 (ttmt) REVERT: F 288 GLN cc_start: 0.7911 (mt0) cc_final: 0.7132 (mt0) outliers start: 70 outliers final: 34 residues processed: 395 average time/residue: 1.1772 time to fit residues: 515.9418 Evaluate side-chains 377 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 341 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 120 optimal weight: 0.9990 chunk 185 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 34 optimal weight: 0.0070 chunk 145 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 283 HIS C 283 HIS D 283 HIS E 133 GLN E 263 ASN E 283 HIS F 133 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.271529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.257000 restraints weight = 13438.673| |-----------------------------------------------------------------------------| r_work (start): 0.4950 rms_B_bonded: 0.83 r_work: 0.4871 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.4776 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.4776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15084 Z= 0.134 Angle : 0.667 8.372 20472 Z= 0.307 Chirality : 0.047 0.165 2406 Planarity : 0.003 0.026 2568 Dihedral : 15.810 172.971 2152 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.74 % Allowed : 22.53 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.19), residues: 1884 helix: 1.47 (0.19), residues: 750 sheet: -0.90 (0.23), residues: 492 loop : -0.18 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 154 HIS 0.004 0.001 HIS A 12 PHE 0.010 0.001 PHE B 313 TYR 0.008 0.001 TYR B 245 ARG 0.003 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 660) hydrogen bonds : angle 4.40381 ( 1800) covalent geometry : bond 0.00286 (15084) covalent geometry : angle 0.66748 (20472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 332 time to evaluate : 1.520 Fit side-chains REVERT: A 26 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6947 (tp30) REVERT: A 78 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6916 (ttmt) REVERT: A 302 ARG cc_start: 0.7128 (mpt180) cc_final: 0.6846 (mpt180) REVERT: C 176 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6939 (mttp) REVERT: D 176 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6906 (mttp) REVERT: F 78 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6847 (ttmt) outliers start: 76 outliers final: 37 residues processed: 379 average time/residue: 1.1444 time to fit residues: 481.0891 Evaluate side-chains 364 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 323 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 176 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 142 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 283 HIS D 283 HIS E 283 HIS F 133 GLN F 283 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.270595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.256047 restraints weight = 13307.278| |-----------------------------------------------------------------------------| r_work (start): 0.4936 rms_B_bonded: 0.83 r_work: 0.4876 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.4781 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.4781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15084 Z= 0.129 Angle : 0.662 8.375 20472 Z= 0.301 Chirality : 0.047 0.168 2406 Planarity : 0.003 0.024 2568 Dihedral : 15.477 176.680 2150 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.99 % Allowed : 23.16 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.19), residues: 1884 helix: 1.45 (0.19), residues: 750 sheet: -1.10 (0.23), residues: 492 loop : -0.21 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 154 HIS 0.003 0.001 HIS D 123 PHE 0.008 0.001 PHE C 313 TYR 0.008 0.001 TYR E 245 ARG 0.007 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.03257 ( 660) hydrogen bonds : angle 4.33653 ( 1800) covalent geometry : bond 0.00281 (15084) covalent geometry : angle 0.66151 (20472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 345 time to evaluate : 1.613 Fit side-chains REVERT: A 302 ARG cc_start: 0.7148 (mpt180) cc_final: 0.6922 (mpt180) REVERT: C 176 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6900 (mttp) REVERT: D 176 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6873 (mttp) REVERT: E 231 HIS cc_start: 0.7457 (m90) cc_final: 0.7227 (m90) REVERT: F 302 ARG cc_start: 0.7271 (mpt180) cc_final: 0.6938 (mpt180) outliers start: 80 outliers final: 33 residues processed: 392 average time/residue: 1.1201 time to fit residues: 488.4690 Evaluate side-chains 361 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 326 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 0.0470 chunk 41 optimal weight: 0.3980 chunk 150 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 65 optimal weight: 0.3980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN B 97 GLN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 12 HIS D 12 HIS E 283 HIS ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.272194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.257702 restraints weight = 13577.900| |-----------------------------------------------------------------------------| r_work (start): 0.4950 rms_B_bonded: 0.83 r_work: 0.4902 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.4810 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.4810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15084 Z= 0.114 Angle : 0.647 8.185 20472 Z= 0.293 Chirality : 0.047 0.163 2406 Planarity : 0.003 0.024 2568 Dihedral : 15.146 177.693 2150 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.43 % Allowed : 23.78 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1884 helix: 1.65 (0.19), residues: 750 sheet: -1.11 (0.23), residues: 492 loop : -0.18 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 154 HIS 0.003 0.001 HIS A 123 PHE 0.006 0.001 PHE D 138 TYR 0.007 0.001 TYR A 245 ARG 0.007 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 660) hydrogen bonds : angle 4.23958 ( 1800) covalent geometry : bond 0.00249 (15084) covalent geometry : angle 0.64671 (20472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 343 time to evaluate : 1.955 Fit side-chains REVERT: A 78 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7134 (tptp) REVERT: B 231 HIS cc_start: 0.7396 (m90) cc_final: 0.7184 (m90) REVERT: C 176 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6790 (mttp) REVERT: D 176 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6767 (mttp) REVERT: E 231 HIS cc_start: 0.7396 (m90) cc_final: 0.7125 (m90) REVERT: F 78 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7089 (tptp) REVERT: F 283 HIS cc_start: 0.7662 (m170) cc_final: 0.7428 (m170) outliers start: 71 outliers final: 34 residues processed: 388 average time/residue: 1.6123 time to fit residues: 692.5273 Evaluate side-chains 369 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 331 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN B 75 ASN B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 HIS D 12 HIS D 123 HIS E 75 ASN E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN F 283 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.267543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.252614 restraints weight = 13494.917| |-----------------------------------------------------------------------------| r_work (start): 0.4908 rms_B_bonded: 0.84 r_work: 0.4859 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.4767 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15084 Z= 0.164 Angle : 0.701 8.530 20472 Z= 0.325 Chirality : 0.048 0.176 2406 Planarity : 0.003 0.026 2568 Dihedral : 14.951 174.311 2150 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.31 % Allowed : 23.91 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.19), residues: 1884 helix: 1.37 (0.19), residues: 750 sheet: -1.38 (0.22), residues: 456 loop : -0.21 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 154 HIS 0.005 0.001 HIS D 12 PHE 0.009 0.002 PHE B 253 TYR 0.012 0.002 TYR D 54 ARG 0.010 0.001 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 660) hydrogen bonds : angle 4.42946 ( 1800) covalent geometry : bond 0.00365 (15084) covalent geometry : angle 0.70116 (20472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 334 time to evaluate : 2.805 Fit side-chains REVERT: A 5 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7619 (mptm) REVERT: A 78 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7150 (tptp) REVERT: B 176 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6772 (mttp) REVERT: B 231 HIS cc_start: 0.7471 (m90) cc_final: 0.7242 (m90) REVERT: C 176 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6887 (mttp) REVERT: D 176 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6832 (mttp) REVERT: D 302 ARG cc_start: 0.7143 (mpt180) cc_final: 0.6923 (mpt180) REVERT: E 231 HIS cc_start: 0.7531 (m90) cc_final: 0.7298 (m90) REVERT: F 78 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7145 (tptp) REVERT: F 224 ASP cc_start: 0.7323 (t0) cc_final: 0.7108 (t0) outliers start: 69 outliers final: 33 residues processed: 375 average time/residue: 1.2752 time to fit residues: 527.0200 Evaluate side-chains 360 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 321 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 151 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 182 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN A 263 ASN B 75 ASN B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN E 75 ASN E 97 GLN E 283 HIS ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.267757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.252900 restraints weight = 13489.032| |-----------------------------------------------------------------------------| r_work (start): 0.4911 rms_B_bonded: 0.85 r_work: 0.4862 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.4771 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.4771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15084 Z= 0.149 Angle : 0.695 8.399 20472 Z= 0.321 Chirality : 0.048 0.173 2406 Planarity : 0.003 0.027 2568 Dihedral : 14.684 174.828 2150 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.18 % Allowed : 24.16 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1884 helix: 1.35 (0.19), residues: 750 sheet: -1.43 (0.22), residues: 456 loop : -0.23 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 154 HIS 0.003 0.001 HIS F 283 PHE 0.007 0.001 PHE E 253 TYR 0.010 0.002 TYR D 54 ARG 0.008 0.001 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 660) hydrogen bonds : angle 4.36758 ( 1800) covalent geometry : bond 0.00331 (15084) covalent geometry : angle 0.69477 (20472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 331 time to evaluate : 1.667 Fit side-chains REVERT: A 78 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7150 (tptp) REVERT: B 176 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6753 (mttp) REVERT: B 231 HIS cc_start: 0.7518 (m90) cc_final: 0.7312 (m90) REVERT: C 176 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6891 (mttp) REVERT: D 176 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6857 (mttp) REVERT: D 302 ARG cc_start: 0.7118 (mpt180) cc_final: 0.6916 (mpt180) REVERT: E 231 HIS cc_start: 0.7527 (m90) cc_final: 0.7322 (m90) REVERT: F 78 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7120 (tptp) outliers start: 67 outliers final: 35 residues processed: 371 average time/residue: 1.1551 time to fit residues: 474.5909 Evaluate side-chains 370 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 330 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 85 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 88 optimal weight: 0.0970 chunk 148 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 263 ASN A 283 HIS B 75 ASN B 283 HIS C 12 HIS C 133 GLN E 75 ASN E 283 HIS ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.268366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.253581 restraints weight = 13437.670| |-----------------------------------------------------------------------------| r_work (start): 0.4916 rms_B_bonded: 0.86 r_work: 0.4867 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.4778 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.4778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15084 Z= 0.136 Angle : 0.692 8.238 20472 Z= 0.317 Chirality : 0.048 0.170 2406 Planarity : 0.003 0.030 2568 Dihedral : 14.434 175.890 2150 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.87 % Allowed : 24.47 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1884 helix: 1.43 (0.19), residues: 750 sheet: -1.44 (0.23), residues: 456 loop : -0.21 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 154 HIS 0.006 0.001 HIS C 12 PHE 0.007 0.001 PHE E 313 TYR 0.012 0.002 TYR A 94 ARG 0.007 0.001 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 660) hydrogen bonds : angle 4.32846 ( 1800) covalent geometry : bond 0.00304 (15084) covalent geometry : angle 0.69226 (20472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 329 time to evaluate : 1.556 Fit side-chains REVERT: A 78 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7160 (tptp) REVERT: A 302 ARG cc_start: 0.7081 (mpt180) cc_final: 0.6701 (mpt90) REVERT: B 176 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6714 (mttp) REVERT: C 176 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6861 (mttp) REVERT: C 281 MET cc_start: 0.8369 (mtp) cc_final: 0.8047 (mtm) REVERT: D 176 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6852 (mttp) REVERT: D 281 MET cc_start: 0.8397 (mtp) cc_final: 0.8074 (mtm) REVERT: E 26 GLU cc_start: 0.7005 (tp30) cc_final: 0.6770 (tp30) REVERT: F 78 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7130 (tptp) outliers start: 62 outliers final: 40 residues processed: 366 average time/residue: 1.1553 time to fit residues: 469.1553 Evaluate side-chains 361 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 316 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 102 LYS Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 139 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 41 optimal weight: 0.0470 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN A 263 ASN A 283 HIS B 75 ASN B 97 GLN B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN C 133 GLN D 75 ASN E 38 GLN E 75 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.263434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.248373 restraints weight = 13343.945| |-----------------------------------------------------------------------------| r_work (start): 0.4876 rms_B_bonded: 0.85 r_work: 0.4825 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.4738 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.4738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15084 Z= 0.221 Angle : 0.769 8.819 20472 Z= 0.363 Chirality : 0.051 0.179 2406 Planarity : 0.004 0.032 2568 Dihedral : 14.318 158.612 2150 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.87 % Allowed : 24.66 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1884 helix: 0.66 (0.19), residues: 792 sheet: -1.69 (0.22), residues: 456 loop : -0.50 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 154 HIS 0.004 0.001 HIS F 12 PHE 0.012 0.002 PHE F 253 TYR 0.020 0.003 TYR D 54 ARG 0.008 0.001 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 660) hydrogen bonds : angle 4.55010 ( 1800) covalent geometry : bond 0.00496 (15084) covalent geometry : angle 0.76882 (20472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 327 time to evaluate : 1.803 Fit side-chains REVERT: A 78 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7177 (tptp) REVERT: A 224 ASP cc_start: 0.7528 (t0) cc_final: 0.7303 (t0) REVERT: C 176 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6797 (mttp) REVERT: D 99 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7988 (ptpt) REVERT: D 176 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6813 (mttp) REVERT: E 3 ASN cc_start: 0.6308 (m-40) cc_final: 0.6105 (m110) REVERT: F 34 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6956 (tptp) REVERT: F 78 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7168 (tptp) REVERT: F 298 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6679 (mp0) outliers start: 62 outliers final: 40 residues processed: 367 average time/residue: 1.1802 time to fit residues: 480.8107 Evaluate side-chains 371 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 324 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 102 LYS Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Chi-restraints excluded: chain F residue 298 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 56 optimal weight: 0.0040 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 0.0670 overall best weight: 0.5332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN A 283 HIS B 283 HIS ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN E 97 GLN E 283 HIS ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 283 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.269530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.254793 restraints weight = 13633.928| |-----------------------------------------------------------------------------| r_work (start): 0.4933 rms_B_bonded: 0.83 r_work: 0.4886 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.4804 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.4804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15084 Z= 0.127 Angle : 0.696 8.126 20472 Z= 0.320 Chirality : 0.048 0.167 2406 Planarity : 0.004 0.048 2568 Dihedral : 14.064 169.594 2150 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.12 % Allowed : 25.47 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1884 helix: 1.28 (0.19), residues: 750 sheet: -1.63 (0.23), residues: 456 loop : -0.22 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 154 HIS 0.003 0.001 HIS A 123 PHE 0.006 0.001 PHE C 138 TYR 0.018 0.002 TYR A 94 ARG 0.010 0.001 ARG C 302 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 660) hydrogen bonds : angle 4.31421 ( 1800) covalent geometry : bond 0.00282 (15084) covalent geometry : angle 0.69629 (20472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 322 time to evaluate : 1.590 Fit side-chains REVERT: A 78 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7152 (tptp) REVERT: C 176 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6849 (mttp) REVERT: C 281 MET cc_start: 0.8403 (mtp) cc_final: 0.8038 (mtm) REVERT: D 176 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6823 (mttp) REVERT: D 281 MET cc_start: 0.8423 (mtp) cc_final: 0.8065 (mtm) REVERT: D 302 ARG cc_start: 0.7023 (mpt180) cc_final: 0.6817 (mpt180) REVERT: E 26 GLU cc_start: 0.6929 (tp30) cc_final: 0.6678 (tp30) REVERT: F 78 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7127 (tptp) outliers start: 50 outliers final: 34 residues processed: 353 average time/residue: 1.1637 time to fit residues: 455.8028 Evaluate side-chains 357 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 319 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN A 263 ASN A 283 HIS B 75 ASN B 97 GLN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN E 75 ASN E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 158 ASN F 283 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.263819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.248791 restraints weight = 13380.887| |-----------------------------------------------------------------------------| r_work (start): 0.4878 rms_B_bonded: 0.86 r_work: 0.4828 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.4741 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.4741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15084 Z= 0.206 Angle : 0.762 8.599 20472 Z= 0.359 Chirality : 0.050 0.175 2406 Planarity : 0.004 0.056 2568 Dihedral : 14.019 158.155 2149 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.00 % Allowed : 25.72 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 1884 helix: 0.66 (0.19), residues: 792 sheet: -1.73 (0.22), residues: 456 loop : -0.53 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 154 HIS 0.005 0.001 HIS F 283 PHE 0.011 0.002 PHE F 253 TYR 0.025 0.003 TYR A 94 ARG 0.013 0.001 ARG C 302 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 660) hydrogen bonds : angle 4.51596 ( 1800) covalent geometry : bond 0.00464 (15084) covalent geometry : angle 0.76181 (20472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13629.86 seconds wall clock time: 235 minutes 27.35 seconds (14127.35 seconds total)