Starting phenix.real_space_refine on Wed Jan 14 01:55:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x56_33009/01_2026/7x56_33009.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x56_33009/01_2026/7x56_33009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x56_33009/01_2026/7x56_33009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x56_33009/01_2026/7x56_33009.map" model { file = "/net/cci-nas-00/data/ceres_data/7x56_33009/01_2026/7x56_33009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x56_33009/01_2026/7x56_33009.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.011 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 10 5.49 5 Mg 5 5.21 5 S 40 5.16 5 C 7370 2.51 5 N 1900 2.21 5 O 2255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11580 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "B" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "C" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "E" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.60, per 1000 atoms: 0.22 Number of scatterers: 11580 At special positions: 0 Unit cell: (77.43, 95.7, 160.08, 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 40 16.00 P 10 15.00 Mg 5 11.99 O 2255 8.00 N 1900 7.00 C 7370 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: 0.91 Conformation dependent library (CDL) restraints added in 561.1 milliseconds 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2670 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 15 sheets defined 35.4% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 67 through 78 removed outlier: 3.504A pdb=" N LEU A 71 " --> pdb=" O MET A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.527A pdb=" N GLU A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 139 removed outlier: 4.139A pdb=" N TYR A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.678A pdb=" N LYS A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.599A pdb=" N PHE A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 214 through 227 removed outlier: 3.914A pdb=" N TYR A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.900A pdb=" N LEU A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.586A pdb=" N GLU A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.703A pdb=" N ALA A 276 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 78 removed outlier: 3.503A pdb=" N LEU B 71 " --> pdb=" O MET B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.527A pdb=" N GLU B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 139 removed outlier: 4.139A pdb=" N TYR B 138 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.678A pdb=" N LYS B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.599A pdb=" N PHE B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 208 Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.914A pdb=" N TYR B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.900A pdb=" N LEU B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.586A pdb=" N GLU B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 269 No H-bonds generated for 'chain 'B' and resid 267 through 269' Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.703A pdb=" N ALA B 276 " --> pdb=" O ASN B 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 78 removed outlier: 3.503A pdb=" N LEU C 71 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 107 removed outlier: 3.527A pdb=" N GLU C 104 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 removed outlier: 4.139A pdb=" N TYR C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.677A pdb=" N LYS C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 191 removed outlier: 3.599A pdb=" N PHE C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'C' and resid 214 through 227 removed outlier: 3.914A pdb=" N TYR C 218 " --> pdb=" O ASP C 214 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 221 " --> pdb=" O GLN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.899A pdb=" N LEU C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.586A pdb=" N GLU C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 269 No H-bonds generated for 'chain 'C' and resid 267 through 269' Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.702A pdb=" N ALA C 276 " --> pdb=" O ASN C 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 78 removed outlier: 3.504A pdb=" N LEU D 71 " --> pdb=" O MET D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 107 removed outlier: 3.527A pdb=" N GLU D 104 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 139 removed outlier: 4.138A pdb=" N TYR D 138 " --> pdb=" O TYR D 134 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 removed outlier: 3.678A pdb=" N LYS D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.599A pdb=" N PHE D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 208 Processing helix chain 'D' and resid 214 through 227 removed outlier: 3.914A pdb=" N TYR D 218 " --> pdb=" O ASP D 214 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.899A pdb=" N LEU D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.586A pdb=" N GLU D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 270 through 285 removed outlier: 3.702A pdb=" N ALA D 276 " --> pdb=" O ASN D 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 78 removed outlier: 3.503A pdb=" N LEU E 71 " --> pdb=" O MET E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 107 removed outlier: 3.527A pdb=" N GLU E 104 " --> pdb=" O THR E 100 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR E 105 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 139 removed outlier: 4.139A pdb=" N TYR E 138 " --> pdb=" O TYR E 134 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.677A pdb=" N LYS E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 191 removed outlier: 3.599A pdb=" N PHE E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 214 through 227 removed outlier: 3.914A pdb=" N TYR E 218 " --> pdb=" O ASP E 214 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE E 221 " --> pdb=" O GLN E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 249 removed outlier: 3.900A pdb=" N LEU E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 255 removed outlier: 3.586A pdb=" N GLU E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 269 No H-bonds generated for 'chain 'E' and resid 267 through 269' Processing helix chain 'E' and resid 270 through 285 removed outlier: 3.702A pdb=" N ALA E 276 " --> pdb=" O ASN E 272 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 24 removed outlier: 4.355A pdb=" N LYS A 2 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 6 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 90 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE A 85 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 127 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU A 87 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL A 129 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A 89 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU A 91 " --> pdb=" O PRO A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 4.464A pdb=" N GLN A 39 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 176 removed outlier: 6.483A pdb=" N VAL A 163 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR A 172 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 161 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR A 174 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 159 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 21 through 24 removed outlier: 4.354A pdb=" N LYS B 2 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 6 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 90 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE B 85 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 127 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 87 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL B 129 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU B 89 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU B 91 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 28 removed outlier: 4.464A pdb=" N GLN B 39 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 176 removed outlier: 6.483A pdb=" N VAL B 163 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR B 172 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 161 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 174 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 159 " --> pdb=" O THR B 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 24 removed outlier: 4.355A pdb=" N LYS C 2 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 6 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU C 90 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE C 85 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C 127 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU C 87 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL C 129 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU C 89 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU C 91 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 27 through 28 removed outlier: 4.464A pdb=" N GLN C 39 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 169 through 176 removed outlier: 6.483A pdb=" N VAL C 163 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR C 172 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 161 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR C 174 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 159 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 21 through 24 removed outlier: 4.354A pdb=" N LYS D 2 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 6 " --> pdb=" O THR D 88 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU D 90 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE D 85 " --> pdb=" O ASN D 125 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU D 127 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU D 87 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL D 129 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU D 89 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU D 91 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 27 through 28 removed outlier: 4.463A pdb=" N GLN D 39 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 169 through 176 removed outlier: 6.483A pdb=" N VAL D 163 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR D 172 " --> pdb=" O ILE D 161 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE D 161 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR D 174 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE D 159 " --> pdb=" O THR D 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 21 through 24 removed outlier: 4.355A pdb=" N LYS E 2 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL E 6 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU E 90 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE E 85 " --> pdb=" O ASN E 125 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU E 127 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU E 87 " --> pdb=" O LEU E 127 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL E 129 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU E 89 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU E 91 " --> pdb=" O PRO E 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.463A pdb=" N GLN E 39 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 169 through 176 removed outlier: 6.483A pdb=" N VAL E 163 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR E 172 " --> pdb=" O ILE E 161 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE E 161 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR E 174 " --> pdb=" O ILE E 159 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE E 159 " --> pdb=" O THR E 174 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3676 1.34 - 1.46: 2403 1.46 - 1.58: 5591 1.58 - 1.69: 15 1.69 - 1.81: 70 Bond restraints: 11755 Sorted by residual: bond pdb=" CA TYR A 15 " pdb=" C TYR A 15 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.20e-02 6.94e+03 3.37e+00 bond pdb=" CA TYR E 15 " pdb=" C TYR E 15 " ideal model delta sigma weight residual 1.522 1.501 0.021 1.20e-02 6.94e+03 3.17e+00 bond pdb=" CA TYR B 15 " pdb=" C TYR B 15 " ideal model delta sigma weight residual 1.522 1.502 0.021 1.20e-02 6.94e+03 3.04e+00 bond pdb=" CA TYR D 15 " pdb=" C TYR D 15 " ideal model delta sigma weight residual 1.522 1.502 0.021 1.20e-02 6.94e+03 3.01e+00 bond pdb=" CA TYR C 15 " pdb=" C TYR C 15 " ideal model delta sigma weight residual 1.522 1.502 0.020 1.20e-02 6.94e+03 2.84e+00 ... (remaining 11750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 14841 1.01 - 2.02: 797 2.02 - 3.02: 130 3.02 - 4.03: 57 4.03 - 5.04: 25 Bond angle restraints: 15850 Sorted by residual: angle pdb=" CA GLU C 278 " pdb=" CB GLU C 278 " pdb=" CG GLU C 278 " ideal model delta sigma weight residual 114.10 118.41 -4.31 2.00e+00 2.50e-01 4.65e+00 angle pdb=" CA GLU D 278 " pdb=" CB GLU D 278 " pdb=" CG GLU D 278 " ideal model delta sigma weight residual 114.10 118.40 -4.30 2.00e+00 2.50e-01 4.62e+00 angle pdb=" CA GLU E 278 " pdb=" CB GLU E 278 " pdb=" CG GLU E 278 " ideal model delta sigma weight residual 114.10 118.40 -4.30 2.00e+00 2.50e-01 4.61e+00 angle pdb=" CA GLU A 278 " pdb=" CB GLU A 278 " pdb=" CG GLU A 278 " ideal model delta sigma weight residual 114.10 118.40 -4.30 2.00e+00 2.50e-01 4.61e+00 angle pdb=" CA GLU B 278 " pdb=" CB GLU B 278 " pdb=" CG GLU B 278 " ideal model delta sigma weight residual 114.10 118.37 -4.27 2.00e+00 2.50e-01 4.57e+00 ... (remaining 15845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 6451 14.03 - 28.06: 524 28.06 - 42.09: 135 42.09 - 56.12: 30 56.12 - 70.15: 15 Dihedral angle restraints: 7155 sinusoidal: 2985 harmonic: 4170 Sorted by residual: dihedral pdb=" CA TYR C 66 " pdb=" C TYR C 66 " pdb=" N MET C 67 " pdb=" CA MET C 67 " ideal model delta harmonic sigma weight residual -180.00 -157.68 -22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA TYR E 66 " pdb=" C TYR E 66 " pdb=" N MET E 67 " pdb=" CA MET E 67 " ideal model delta harmonic sigma weight residual -180.00 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA TYR A 66 " pdb=" C TYR A 66 " pdb=" N MET A 67 " pdb=" CA MET A 67 " ideal model delta harmonic sigma weight residual 180.00 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 992 0.025 - 0.050: 518 0.050 - 0.075: 116 0.075 - 0.100: 100 0.100 - 0.125: 69 Chirality restraints: 1795 Sorted by residual: chirality pdb=" CA ILE D 211 " pdb=" N ILE D 211 " pdb=" C ILE D 211 " pdb=" CB ILE D 211 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE B 175 " pdb=" N ILE B 175 " pdb=" C ILE B 175 " pdb=" CB ILE B 175 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE D 175 " pdb=" N ILE D 175 " pdb=" C ILE D 175 " pdb=" CB ILE D 175 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1792 not shown) Planarity restraints: 1980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 14 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C LYS D 14 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS D 14 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR D 15 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 14 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C LYS B 14 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS B 14 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR B 15 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 14 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C LYS E 14 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS E 14 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR E 15 " 0.011 2.00e-02 2.50e+03 ... (remaining 1977 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 224 2.61 - 3.18: 10822 3.18 - 3.75: 16314 3.75 - 4.33: 24843 4.33 - 4.90: 41324 Nonbonded interactions: 93527 Sorted by model distance: nonbonded pdb=" O1B GDP A 300 " pdb="MG MG A 301 " model vdw 2.032 2.170 nonbonded pdb=" O1B GDP E 300 " pdb="MG MG E 301 " model vdw 2.032 2.170 nonbonded pdb=" O1B GDP B 300 " pdb="MG MG B 301 " model vdw 2.033 2.170 nonbonded pdb=" O1B GDP D 300 " pdb="MG MG D 301 " model vdw 2.033 2.170 nonbonded pdb=" O1B GDP C 300 " pdb="MG MG C 301 " model vdw 2.033 2.170 ... (remaining 93522 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.200 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.004 0.031 11755 Z= 0.188 Angle : 0.576 5.041 15850 Z= 0.303 Chirality : 0.041 0.125 1795 Planarity : 0.003 0.020 1980 Dihedral : 11.847 70.152 4485 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.23), residues: 1415 helix: -0.40 (0.29), residues: 350 sheet: -1.60 (0.29), residues: 365 loop : -1.32 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 204 TYR 0.008 0.001 TYR C 72 PHE 0.008 0.001 PHE E 59 TRP 0.003 0.001 TRP D 284 HIS 0.003 0.002 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00422 (11755) covalent geometry : angle 0.57607 (15850) hydrogen bonds : bond 0.17289 ( 395) hydrogen bonds : angle 7.12218 ( 1125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.470 Fit side-chains REVERT: B 219 ILE cc_start: 0.8430 (mm) cc_final: 0.8108 (mt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.0933 time to fit residues: 20.2758 Evaluate side-chains 95 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN C 69 GLN C 203 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.094435 restraints weight = 21945.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096895 restraints weight = 11674.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098557 restraints weight = 7300.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099649 restraints weight = 5053.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100447 restraints weight = 3795.153| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11755 Z= 0.227 Angle : 0.673 5.302 15850 Z= 0.350 Chirality : 0.049 0.154 1795 Planarity : 0.004 0.035 1980 Dihedral : 6.414 52.882 1595 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.78 % Allowed : 5.73 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.24), residues: 1415 helix: -0.18 (0.27), residues: 365 sheet: -1.28 (0.29), residues: 400 loop : -1.29 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 57 TYR 0.014 0.002 TYR B 218 PHE 0.014 0.002 PHE B 59 TRP 0.011 0.002 TRP D 284 HIS 0.008 0.005 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00533 (11755) covalent geometry : angle 0.67328 (15850) hydrogen bonds : bond 0.03020 ( 395) hydrogen bonds : angle 5.40099 ( 1125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.475 Fit side-chains REVERT: B 96 MET cc_start: 0.8662 (mmm) cc_final: 0.8433 (mmm) REVERT: E 219 ILE cc_start: 0.8772 (mm) cc_final: 0.8502 (mt) outliers start: 10 outliers final: 7 residues processed: 135 average time/residue: 0.0916 time to fit residues: 18.8460 Evaluate side-chains 116 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain E residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 109 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN C 69 GLN ** C 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.103444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.093133 restraints weight = 22270.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.095739 restraints weight = 11588.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097452 restraints weight = 7147.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.098608 restraints weight = 4911.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099417 restraints weight = 3648.519| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11755 Z= 0.204 Angle : 0.620 5.299 15850 Z= 0.321 Chirality : 0.046 0.146 1795 Planarity : 0.004 0.048 1980 Dihedral : 6.400 52.763 1595 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.33 % Allowed : 8.39 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.23), residues: 1415 helix: -0.13 (0.27), residues: 365 sheet: -1.08 (0.29), residues: 395 loop : -1.37 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 57 TYR 0.013 0.002 TYR C 218 PHE 0.014 0.002 PHE B 59 TRP 0.006 0.001 TRP C 284 HIS 0.006 0.004 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00479 (11755) covalent geometry : angle 0.62010 (15850) hydrogen bonds : bond 0.02890 ( 395) hydrogen bonds : angle 5.24098 ( 1125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 176 LYS cc_start: 0.7534 (tttt) cc_final: 0.7332 (ttmt) REVERT: E 219 ILE cc_start: 0.8863 (mm) cc_final: 0.8653 (mt) outliers start: 17 outliers final: 13 residues processed: 155 average time/residue: 0.0854 time to fit residues: 20.7804 Evaluate side-chains 131 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 237 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 68 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 61 optimal weight: 0.0370 chunk 36 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 69 GLN B 78 ASN C 78 ASN D 78 ASN D 272 ASN E 69 GLN E 78 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.098856 restraints weight = 21804.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101508 restraints weight = 11334.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.103236 restraints weight = 6919.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.104339 restraints weight = 4710.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.105175 restraints weight = 3513.746| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11755 Z= 0.108 Angle : 0.523 5.224 15850 Z= 0.274 Chirality : 0.043 0.184 1795 Planarity : 0.003 0.022 1980 Dihedral : 6.014 44.489 1595 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.18 % Allowed : 9.88 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.23), residues: 1415 helix: 0.38 (0.28), residues: 365 sheet: -0.71 (0.29), residues: 395 loop : -1.36 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 57 TYR 0.010 0.001 TYR E 218 PHE 0.006 0.001 PHE E 23 TRP 0.011 0.001 TRP C 284 HIS 0.002 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00231 (11755) covalent geometry : angle 0.52256 (15850) hydrogen bonds : bond 0.01893 ( 395) hydrogen bonds : angle 4.78239 ( 1125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.462 Fit side-chains REVERT: B 24 SER cc_start: 0.8669 (t) cc_final: 0.8158 (p) REVERT: E 24 SER cc_start: 0.8560 (t) cc_final: 0.8007 (p) REVERT: E 219 ILE cc_start: 0.8771 (mm) cc_final: 0.8541 (mt) outliers start: 15 outliers final: 11 residues processed: 190 average time/residue: 0.0854 time to fit residues: 25.0568 Evaluate side-chains 149 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain E residue 164 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 19 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN B 203 GLN B 267 ASN C 144 ASN C 267 ASN D 144 ASN D 267 ASN D 272 ASN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN E 267 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.101548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.091267 restraints weight = 22289.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.093834 restraints weight = 11676.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095515 restraints weight = 7200.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096664 restraints weight = 4966.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097408 restraints weight = 3703.854| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11755 Z= 0.261 Angle : 0.674 6.145 15850 Z= 0.348 Chirality : 0.048 0.180 1795 Planarity : 0.004 0.062 1980 Dihedral : 6.511 58.638 1595 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.73 % Allowed : 11.37 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.22), residues: 1415 helix: -0.35 (0.25), residues: 400 sheet: -0.93 (0.28), residues: 400 loop : -1.78 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 57 TYR 0.017 0.002 TYR A 72 PHE 0.019 0.002 PHE B 59 TRP 0.013 0.003 TRP D 284 HIS 0.008 0.005 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00622 (11755) covalent geometry : angle 0.67389 (15850) hydrogen bonds : bond 0.02788 ( 395) hydrogen bonds : angle 5.18437 ( 1125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.532 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 146 average time/residue: 0.0805 time to fit residues: 18.3573 Evaluate side-chains 136 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain E residue 237 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 28 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.103455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.093187 restraints weight = 21997.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.095801 restraints weight = 11455.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097503 restraints weight = 7023.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098665 restraints weight = 4812.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099484 restraints weight = 3555.889| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11755 Z= 0.176 Angle : 0.587 5.326 15850 Z= 0.307 Chirality : 0.045 0.172 1795 Planarity : 0.003 0.039 1980 Dihedral : 6.328 54.735 1595 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.88 % Allowed : 12.24 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.22), residues: 1415 helix: -0.35 (0.24), residues: 430 sheet: -0.76 (0.29), residues: 385 loop : -2.10 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 57 TYR 0.012 0.002 TYR D 218 PHE 0.012 0.001 PHE B 59 TRP 0.010 0.002 TRP A 284 HIS 0.006 0.003 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00409 (11755) covalent geometry : angle 0.58714 (15850) hydrogen bonds : bond 0.02205 ( 395) hydrogen bonds : angle 4.93941 ( 1125) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.489 Fit side-chains REVERT: B 278 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6626 (mm-30) REVERT: E 24 SER cc_start: 0.8578 (t) cc_final: 0.8065 (p) outliers start: 24 outliers final: 16 residues processed: 154 average time/residue: 0.0919 time to fit residues: 21.6808 Evaluate side-chains 147 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 237 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN B 260 ASN C 260 ASN D 260 ASN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.098992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.088728 restraints weight = 22575.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.091240 restraints weight = 11844.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092856 restraints weight = 7341.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.093995 restraints weight = 5132.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.094786 restraints weight = 3843.558| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 11755 Z= 0.335 Angle : 0.740 5.673 15850 Z= 0.381 Chirality : 0.050 0.169 1795 Planarity : 0.005 0.065 1980 Dihedral : 6.873 65.773 1595 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 1.96 % Allowed : 12.47 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.21), residues: 1415 helix: -0.68 (0.23), residues: 430 sheet: -0.89 (0.29), residues: 385 loop : -2.19 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 57 TYR 0.014 0.002 TYR D 218 PHE 0.022 0.002 PHE D 59 TRP 0.009 0.002 TRP B 284 HIS 0.009 0.005 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00795 (11755) covalent geometry : angle 0.74034 (15850) hydrogen bonds : bond 0.03121 ( 395) hydrogen bonds : angle 5.36205 ( 1125) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.391 Fit side-chains REVERT: B 278 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6659 (mm-30) outliers start: 25 outliers final: 17 residues processed: 134 average time/residue: 0.0815 time to fit residues: 17.1527 Evaluate side-chains 132 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 237 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 8 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.101935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.091873 restraints weight = 22112.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094367 restraints weight = 11679.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.096013 restraints weight = 7251.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097072 restraints weight = 5021.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097878 restraints weight = 3807.731| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11755 Z= 0.199 Angle : 0.621 5.964 15850 Z= 0.324 Chirality : 0.046 0.164 1795 Planarity : 0.004 0.031 1980 Dihedral : 6.558 59.408 1595 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.80 % Allowed : 12.78 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.21), residues: 1415 helix: -0.46 (0.24), residues: 430 sheet: -0.81 (0.29), residues: 385 loop : -2.16 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 57 TYR 0.015 0.002 TYR D 72 PHE 0.012 0.001 PHE C 59 TRP 0.008 0.002 TRP B 284 HIS 0.006 0.004 HIS E 265 Details of bonding type rmsd covalent geometry : bond 0.00468 (11755) covalent geometry : angle 0.62090 (15850) hydrogen bonds : bond 0.02417 ( 395) hydrogen bonds : angle 5.06250 ( 1125) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.563 Fit side-chains REVERT: B 96 MET cc_start: 0.8871 (mmm) cc_final: 0.8610 (mmm) REVERT: B 278 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6595 (mm-30) outliers start: 23 outliers final: 19 residues processed: 154 average time/residue: 0.0920 time to fit residues: 21.8445 Evaluate side-chains 147 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 237 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.095022 restraints weight = 21767.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097563 restraints weight = 11461.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099217 restraints weight = 7046.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.100340 restraints weight = 4839.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101134 restraints weight = 3594.560| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11755 Z= 0.135 Angle : 0.573 6.009 15850 Z= 0.303 Chirality : 0.044 0.162 1795 Planarity : 0.003 0.023 1980 Dihedral : 6.222 52.316 1595 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.80 % Allowed : 13.25 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.22), residues: 1415 helix: -0.15 (0.25), residues: 430 sheet: -0.67 (0.29), residues: 385 loop : -2.04 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 57 TYR 0.012 0.001 TYR E 238 PHE 0.008 0.001 PHE B 242 TRP 0.006 0.001 TRP D 284 HIS 0.004 0.002 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00303 (11755) covalent geometry : angle 0.57261 (15850) hydrogen bonds : bond 0.01927 ( 395) hydrogen bonds : angle 4.73636 ( 1125) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.378 Fit side-chains REVERT: B 24 SER cc_start: 0.8600 (t) cc_final: 0.8094 (p) REVERT: B 96 MET cc_start: 0.8892 (mmm) cc_final: 0.8681 (mmm) REVERT: E 24 SER cc_start: 0.8552 (t) cc_final: 0.8044 (p) outliers start: 23 outliers final: 18 residues processed: 160 average time/residue: 0.0837 time to fit residues: 20.3761 Evaluate side-chains 150 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 164 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 84 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 14 optimal weight: 0.0670 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.101927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.091452 restraints weight = 22380.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.093999 restraints weight = 12099.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.095709 restraints weight = 7578.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.096881 restraints weight = 5257.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097690 restraints weight = 3924.311| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11755 Z= 0.166 Angle : 0.608 7.006 15850 Z= 0.319 Chirality : 0.046 0.208 1795 Planarity : 0.003 0.043 1980 Dihedral : 6.263 54.835 1595 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.33 % Allowed : 14.04 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.22), residues: 1415 helix: -0.15 (0.24), residues: 430 sheet: -0.71 (0.29), residues: 390 loop : -1.94 (0.22), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 57 TYR 0.011 0.001 TYR E 238 PHE 0.009 0.001 PHE D 59 TRP 0.007 0.001 TRP B 284 HIS 0.005 0.003 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00385 (11755) covalent geometry : angle 0.60782 (15850) hydrogen bonds : bond 0.02181 ( 395) hydrogen bonds : angle 4.73479 ( 1125) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.298 Fit side-chains REVERT: B 96 MET cc_start: 0.8916 (mmm) cc_final: 0.8698 (mmm) REVERT: B 278 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6077 (mm-30) REVERT: E 24 SER cc_start: 0.8596 (t) cc_final: 0.8074 (p) outliers start: 17 outliers final: 14 residues processed: 146 average time/residue: 0.0883 time to fit residues: 20.0286 Evaluate side-chains 143 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain E residue 164 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 97 optimal weight: 0.0770 chunk 36 optimal weight: 10.0000 chunk 50 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN E 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.105226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.094695 restraints weight = 22044.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097371 restraints weight = 11570.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099155 restraints weight = 7108.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.100375 restraints weight = 4837.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.101229 restraints weight = 3534.906| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11755 Z= 0.116 Angle : 0.567 7.643 15850 Z= 0.300 Chirality : 0.044 0.208 1795 Planarity : 0.003 0.024 1980 Dihedral : 5.998 47.992 1595 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.94 % Allowed : 14.59 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.22), residues: 1415 helix: 0.06 (0.25), residues: 430 sheet: -0.67 (0.29), residues: 395 loop : -1.88 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 57 TYR 0.013 0.001 TYR D 72 PHE 0.007 0.001 PHE B 242 TRP 0.005 0.001 TRP B 284 HIS 0.003 0.002 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00247 (11755) covalent geometry : angle 0.56654 (15850) hydrogen bonds : bond 0.01758 ( 395) hydrogen bonds : angle 4.49672 ( 1125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1451.48 seconds wall clock time: 26 minutes 30.52 seconds (1590.52 seconds total)