Starting phenix.real_space_refine on Tue Nov 18 03:49:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6f95_4196/11_2025/6f95_4196.cif Found real_map, /net/cci-nas-00/data/ceres_data/6f95_4196/11_2025/6f95_4196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6f95_4196/11_2025/6f95_4196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6f95_4196/11_2025/6f95_4196.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6f95_4196/11_2025/6f95_4196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6f95_4196/11_2025/6f95_4196.map" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 65 5.16 5 C 6750 2.51 5 N 1690 2.21 5 O 2115 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-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10635 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2099 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "B" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2099 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "C" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2099 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "D" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2099 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "E" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2099 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.54, per 1000 atoms: 0.24 Number of scatterers: 10635 At special positions: 0 Unit cell: (94.16, 92.02, 175.48, 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 65 16.00 P 10 15.00 Mg 5 11.99 O 2115 8.00 N 1690 7.00 C 6750 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: 0.99 Conformation dependent library (CDL) restraints added in 414.8 milliseconds 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 27.3% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 60 through 66 removed outlier: 3.885A pdb=" N PHE A 66 " --> pdb=" O ASN A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.866A pdb=" N MET A 72 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.948A pdb=" N LEU A 88 " --> pdb=" O GLY A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.608A pdb=" N LYS A 120 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.825A pdb=" N ASN A 157 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.829A pdb=" N LYS A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 236 removed outlier: 4.122A pdb=" N GLU A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 256 through 264 removed outlier: 4.252A pdb=" N LEU A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 66 removed outlier: 3.885A pdb=" N PHE B 66 " --> pdb=" O ASN B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 removed outlier: 3.867A pdb=" N MET B 72 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 97 removed outlier: 3.948A pdb=" N LEU B 88 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 removed outlier: 3.607A pdb=" N LYS B 120 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.826A pdb=" N ASN B 157 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 212 removed outlier: 3.830A pdb=" N LYS B 206 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 236 removed outlier: 4.122A pdb=" N GLU B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 256 through 264 removed outlier: 4.253A pdb=" N LEU B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 removed outlier: 3.885A pdb=" N PHE C 66 " --> pdb=" O ASN C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.866A pdb=" N MET C 72 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 97 removed outlier: 3.948A pdb=" N LEU C 88 " --> pdb=" O GLY C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.607A pdb=" N LYS C 120 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.826A pdb=" N ASN C 157 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 212 removed outlier: 3.829A pdb=" N LYS C 206 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 236 removed outlier: 4.121A pdb=" N GLU C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 264 removed outlier: 4.253A pdb=" N LEU C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 66 removed outlier: 3.884A pdb=" N PHE D 66 " --> pdb=" O ASN D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 72 removed outlier: 3.867A pdb=" N MET D 72 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 97 removed outlier: 3.948A pdb=" N LEU D 88 " --> pdb=" O GLY D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 removed outlier: 3.608A pdb=" N LYS D 120 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 159 removed outlier: 3.826A pdb=" N ASN D 157 " --> pdb=" O GLY D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 212 removed outlier: 3.829A pdb=" N LYS D 206 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 236 removed outlier: 4.121A pdb=" N GLU D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 264 removed outlier: 4.253A pdb=" N LEU D 262 " --> pdb=" O ASN D 258 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 66 removed outlier: 3.885A pdb=" N PHE E 66 " --> pdb=" O ASN E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 removed outlier: 3.868A pdb=" N MET E 72 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 97 removed outlier: 3.949A pdb=" N LEU E 88 " --> pdb=" O GLY E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.607A pdb=" N LYS E 120 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 159 removed outlier: 3.826A pdb=" N ASN E 157 " --> pdb=" O GLY E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 212 removed outlier: 3.829A pdb=" N LYS E 206 " --> pdb=" O MET E 202 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS E 210 " --> pdb=" O LYS E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 236 removed outlier: 4.122A pdb=" N GLU E 233 " --> pdb=" O GLU E 229 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS E 234 " --> pdb=" O GLU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 256 through 264 removed outlier: 4.253A pdb=" N LEU E 262 " --> pdb=" O ASN E 258 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 3.848A pdb=" N THR A 109 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE A 9 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS A 144 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU A 106 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE A 146 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 108 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET A 148 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N CYS A 110 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A 150 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS A 34 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 193 removed outlier: 6.382A pdb=" N VAL A 165 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR A 224 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL A 167 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 30 removed outlier: 3.848A pdb=" N THR B 109 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE B 9 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS B 144 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU B 106 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE B 146 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 108 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET B 148 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N CYS B 110 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA B 150 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 34 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 192 through 193 removed outlier: 6.383A pdb=" N VAL B 165 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR B 224 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 167 " --> pdb=" O THR B 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 30 removed outlier: 3.847A pdb=" N THR C 109 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE C 9 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS C 144 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU C 106 " --> pdb=" O HIS C 144 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE C 146 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU C 108 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET C 148 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N CYS C 110 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA C 150 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS C 34 " --> pdb=" O TYR C 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 192 through 193 removed outlier: 6.382A pdb=" N VAL C 165 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR C 224 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL C 167 " --> pdb=" O THR C 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 30 removed outlier: 3.849A pdb=" N THR D 109 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE D 9 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS D 144 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU D 106 " --> pdb=" O HIS D 144 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE D 146 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU D 108 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET D 148 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N CYS D 110 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA D 150 " --> pdb=" O CYS D 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS D 34 " --> pdb=" O TYR D 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 192 through 193 removed outlier: 6.381A pdb=" N VAL D 165 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR D 224 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL D 167 " --> pdb=" O THR D 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 25 through 30 removed outlier: 3.849A pdb=" N THR E 109 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE E 9 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS E 144 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU E 106 " --> pdb=" O HIS E 144 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE E 146 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU E 108 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET E 148 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N CYS E 110 " --> pdb=" O MET E 148 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA E 150 " --> pdb=" O CYS E 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS E 34 " --> pdb=" O TYR E 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 192 through 193 removed outlier: 6.383A pdb=" N VAL E 165 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR E 224 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL E 167 " --> pdb=" O THR E 224 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 756 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: 1.64 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3333 1.34 - 1.46: 2319 1.46 - 1.57: 5078 1.57 - 1.69: 15 1.69 - 1.81: 105 Bond restraints: 10850 Sorted by residual: bond pdb=" CB ARG A 87 " pdb=" CG ARG A 87 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.98e+00 bond pdb=" CB ARG B 87 " pdb=" CG ARG B 87 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" CB ARG C 87 " pdb=" CG ARG C 87 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CB ARG E 87 " pdb=" CG ARG E 87 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CB ARG D 87 " pdb=" CG ARG D 87 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 ... (remaining 10845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 13540 1.50 - 3.00: 933 3.00 - 4.51: 126 4.51 - 6.01: 49 6.01 - 7.51: 27 Bond angle restraints: 14675 Sorted by residual: angle pdb=" C ARG B 78 " pdb=" N LYS B 79 " pdb=" CA LYS B 79 " ideal model delta sigma weight residual 121.05 125.51 -4.46 1.43e+00 4.89e-01 9.71e+00 angle pdb=" C ARG A 78 " pdb=" N LYS A 79 " pdb=" CA LYS A 79 " ideal model delta sigma weight residual 121.05 125.49 -4.44 1.43e+00 4.89e-01 9.63e+00 angle pdb=" C ARG E 78 " pdb=" N LYS E 79 " pdb=" CA LYS E 79 " ideal model delta sigma weight residual 121.05 125.47 -4.42 1.43e+00 4.89e-01 9.54e+00 angle pdb=" C ARG D 78 " pdb=" N LYS D 79 " pdb=" CA LYS D 79 " ideal model delta sigma weight residual 121.05 125.46 -4.41 1.43e+00 4.89e-01 9.51e+00 angle pdb=" C ARG C 78 " pdb=" N LYS C 79 " pdb=" CA LYS C 79 " ideal model delta sigma weight residual 121.05 125.43 -4.38 1.43e+00 4.89e-01 9.40e+00 ... (remaining 14670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.37: 6304 29.37 - 58.74: 51 58.74 - 88.11: 0 88.11 - 117.48: 5 117.48 - 146.84: 10 Dihedral angle restraints: 6370 sinusoidal: 2510 harmonic: 3860 Sorted by residual: dihedral pdb=" O1B ADP E 302 " pdb=" O3A ADP E 302 " pdb=" PB ADP E 302 " pdb=" PA ADP E 302 " ideal model delta sinusoidal sigma weight residual 300.00 153.15 146.84 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" O1B ADP C 302 " pdb=" O3A ADP C 302 " pdb=" PB ADP C 302 " pdb=" PA ADP C 302 " ideal model delta sinusoidal sigma weight residual 300.00 153.21 146.79 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" O1B ADP A 302 " pdb=" O3A ADP A 302 " pdb=" PB ADP A 302 " pdb=" PA ADP A 302 " ideal model delta sinusoidal sigma weight residual 300.00 153.21 146.78 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 6367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 991 0.044 - 0.089: 436 0.089 - 0.133: 154 0.133 - 0.177: 24 0.177 - 0.222: 5 Chirality restraints: 1610 Sorted by residual: chirality pdb=" CB VAL C 26 " pdb=" CA VAL C 26 " pdb=" CG1 VAL C 26 " pdb=" CG2 VAL C 26 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB VAL B 26 " pdb=" CA VAL B 26 " pdb=" CG1 VAL B 26 " pdb=" CG2 VAL B 26 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB VAL E 26 " pdb=" CA VAL E 26 " pdb=" CG1 VAL E 26 " pdb=" CG2 VAL E 26 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1607 not shown) Planarity restraints: 1850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 252 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO B 253 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 253 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 253 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 252 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO E 253 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 253 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 253 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 252 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO D 253 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 253 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 253 " 0.029 5.00e-02 4.00e+02 ... (remaining 1847 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1825 2.76 - 3.29: 9014 3.29 - 3.83: 17022 3.83 - 4.36: 20553 4.36 - 4.90: 35639 Nonbonded interactions: 84053 Sorted by model distance: nonbonded pdb=" NZ LYS E 15 " pdb=" O3B ADP E 302 " model vdw 2.224 3.120 nonbonded pdb=" OE2 GLU C 131 " pdb=" OG SER C 138 " model vdw 2.296 3.040 nonbonded pdb=" OE2 GLU D 131 " pdb=" OG SER D 138 " model vdw 2.297 3.040 nonbonded pdb=" OE2 GLU E 131 " pdb=" OG SER E 138 " model vdw 2.297 3.040 nonbonded pdb=" OE2 GLU A 131 " pdb=" OG SER A 138 " model vdw 2.298 3.040 ... (remaining 84048 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: 0.03 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.370 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 10850 Z= 0.321 Angle : 0.894 7.509 14675 Z= 0.459 Chirality : 0.055 0.222 1610 Planarity : 0.005 0.053 1850 Dihedral : 12.029 146.845 3940 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.44 % Allowed : 0.44 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.24 (0.19), residues: 1325 helix: -4.70 (0.08), residues: 300 sheet: -1.66 (0.28), residues: 340 loop : -2.49 (0.20), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 68 TYR 0.032 0.003 TYR A 56 PHE 0.028 0.003 PHE C 126 HIS 0.005 0.002 HIS D 81 Details of bonding type rmsd covalent geometry : bond 0.00733 (10850) covalent geometry : angle 0.89374 (14675) hydrogen bonds : bond 0.27283 ( 327) hydrogen bonds : angle 9.93962 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 338 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 THR cc_start: 0.9292 (p) cc_final: 0.8134 (p) REVERT: A 62 LYS cc_start: 0.8850 (pttt) cc_final: 0.8549 (ptmm) REVERT: A 82 MET cc_start: 0.6346 (mmm) cc_final: 0.5678 (pmm) REVERT: A 97 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8300 (ttmm) REVERT: A 139 PHE cc_start: 0.7725 (t80) cc_final: 0.7413 (t80) REVERT: A 161 SER cc_start: 0.8889 (t) cc_final: 0.8675 (p) REVERT: A 258 ASN cc_start: 0.8859 (m-40) cc_final: 0.8530 (m-40) REVERT: B 45 MET cc_start: 0.8875 (ptp) cc_final: 0.8587 (ptp) REVERT: B 82 MET cc_start: 0.6037 (mmm) cc_final: 0.5784 (pmm) REVERT: B 142 THR cc_start: 0.7956 (m) cc_final: 0.7551 (p) REVERT: B 248 LEU cc_start: 0.8679 (mt) cc_final: 0.8022 (mp) REVERT: C 85 GLN cc_start: 0.8387 (mt0) cc_final: 0.8110 (mt0) REVERT: C 202 MET cc_start: 0.8008 (tpp) cc_final: 0.7431 (tpp) REVERT: C 254 SER cc_start: 0.8679 (m) cc_final: 0.8344 (t) REVERT: D 20 ASP cc_start: 0.6746 (p0) cc_final: 0.6475 (p0) REVERT: D 72 MET cc_start: 0.7858 (ptp) cc_final: 0.7469 (ptp) REVERT: D 82 MET cc_start: 0.6458 (mmm) cc_final: 0.6242 (pmm) REVERT: D 186 LYS cc_start: 0.8054 (ttmt) cc_final: 0.7816 (ttmm) REVERT: D 188 ASP cc_start: 0.6909 (m-30) cc_final: 0.6428 (t0) REVERT: D 256 TYR cc_start: 0.8210 (m-80) cc_final: 0.7955 (m-80) REVERT: E 6 VAL cc_start: 0.9552 (OUTLIER) cc_final: 0.9305 (m) REVERT: E 112 TYR cc_start: 0.8702 (t80) cc_final: 0.8146 (t80) REVERT: E 214 ASN cc_start: 0.8743 (p0) cc_final: 0.8527 (p0) REVERT: E 233 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7156 (mt-10) REVERT: E 254 SER cc_start: 0.8843 (m) cc_final: 0.8531 (p) outliers start: 5 outliers final: 1 residues processed: 343 average time/residue: 0.1080 time to fit residues: 51.9700 Evaluate side-chains 174 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain E residue 6 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.0020 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 125 HIS ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN C 11 ASN C 63 ASN C 76 ASN C 125 HIS C 190 HIS D 11 ASN D 125 HIS E 11 ASN E 85 GLN E 125 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.095966 restraints weight = 17923.804| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.40 r_work: 0.3084 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10850 Z= 0.129 Angle : 0.637 8.020 14675 Z= 0.310 Chirality : 0.046 0.137 1610 Planarity : 0.004 0.039 1850 Dihedral : 11.631 115.349 1517 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.71 % Allowed : 8.38 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.21), residues: 1325 helix: -3.44 (0.21), residues: 250 sheet: -1.65 (0.25), residues: 385 loop : -1.75 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 130 TYR 0.015 0.001 TYR E 56 PHE 0.010 0.001 PHE E 158 HIS 0.006 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00280 (10850) covalent geometry : angle 0.63706 (14675) hydrogen bonds : bond 0.03306 ( 327) hydrogen bonds : angle 5.89799 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7103 (mmm) cc_final: 0.6107 (pmm) REVERT: B 82 MET cc_start: 0.6457 (mmm) cc_final: 0.5843 (pmm) REVERT: B 202 MET cc_start: 0.7954 (tpp) cc_final: 0.7616 (tpp) REVERT: B 206 LYS cc_start: 0.8567 (mttt) cc_final: 0.8332 (mtmm) REVERT: B 248 LEU cc_start: 0.8422 (mt) cc_final: 0.7908 (mt) REVERT: C 115 MET cc_start: 0.7054 (mmt) cc_final: 0.6813 (tpp) REVERT: C 202 MET cc_start: 0.8572 (tpp) cc_final: 0.8114 (tpp) REVERT: C 254 SER cc_start: 0.8536 (m) cc_final: 0.8184 (t) REVERT: C 256 TYR cc_start: 0.8581 (m-80) cc_final: 0.8242 (m-80) REVERT: D 135 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6940 (mm-30) REVERT: E 6 VAL cc_start: 0.9548 (OUTLIER) cc_final: 0.9250 (m) REVERT: E 130 ARG cc_start: 0.8083 (tpp-160) cc_final: 0.7624 (tpp-160) outliers start: 31 outliers final: 19 residues processed: 231 average time/residue: 0.1074 time to fit residues: 35.1300 Evaluate side-chains 169 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 147 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 HIS B 76 ASN B 85 GLN B 144 HIS B 190 HIS C 63 ASN C 190 HIS D 85 GLN E 85 GLN E 124 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.087634 restraints weight = 18495.430| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.46 r_work: 0.2968 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10850 Z= 0.230 Angle : 0.678 8.613 14675 Z= 0.330 Chirality : 0.048 0.139 1610 Planarity : 0.004 0.043 1850 Dihedral : 11.524 115.990 1517 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.10 % Allowed : 10.48 % 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: -2.75 (0.21), residues: 1325 helix: -2.58 (0.26), residues: 255 sheet: -1.48 (0.25), residues: 385 loop : -1.64 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 130 TYR 0.017 0.002 TYR B 56 PHE 0.015 0.002 PHE D 158 HIS 0.007 0.002 HIS D 81 Details of bonding type rmsd covalent geometry : bond 0.00531 (10850) covalent geometry : angle 0.67849 (14675) hydrogen bonds : bond 0.03370 ( 327) hydrogen bonds : angle 5.51092 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4221 (OUTLIER) cc_final: 0.2271 (mt-10) REVERT: B 82 MET cc_start: 0.6777 (mmm) cc_final: 0.5989 (pmm) REVERT: B 202 MET cc_start: 0.8165 (tpp) cc_final: 0.7821 (mmt) REVERT: B 206 LYS cc_start: 0.8752 (mttt) cc_final: 0.8518 (mtmm) REVERT: B 233 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8382 (mm-30) REVERT: B 248 LEU cc_start: 0.8522 (mt) cc_final: 0.7751 (mp) REVERT: C 82 MET cc_start: 0.6984 (pmm) cc_final: 0.6003 (ptm) REVERT: C 115 MET cc_start: 0.7087 (mmt) cc_final: 0.6815 (tpp) REVERT: C 158 PHE cc_start: 0.8240 (m-80) cc_final: 0.7811 (m-10) REVERT: C 202 MET cc_start: 0.8517 (tpp) cc_final: 0.7818 (tpt) REVERT: E 130 ARG cc_start: 0.8064 (tpp-160) cc_final: 0.7745 (tpp-160) outliers start: 47 outliers final: 25 residues processed: 191 average time/residue: 0.1068 time to fit residues: 28.9850 Evaluate side-chains 156 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 190 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 7 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN B 76 ASN B 144 HIS B 190 HIS C 190 HIS E 85 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.107662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.089089 restraints weight = 18417.127| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.41 r_work: 0.2991 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10850 Z= 0.161 Angle : 0.607 7.202 14675 Z= 0.295 Chirality : 0.046 0.151 1610 Planarity : 0.004 0.040 1850 Dihedral : 10.958 110.651 1516 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.93 % Allowed : 11.97 % Favored : 84.10 % 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: -2.50 (0.21), residues: 1325 helix: -2.11 (0.29), residues: 255 sheet: -1.27 (0.25), residues: 385 loop : -1.64 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 130 TYR 0.017 0.002 TYR B 56 PHE 0.012 0.001 PHE D 158 HIS 0.008 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00372 (10850) covalent geometry : angle 0.60676 (14675) hydrogen bonds : bond 0.02789 ( 327) hydrogen bonds : angle 5.13545 ( 756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4072 (OUTLIER) cc_final: 0.2308 (mt-10) REVERT: A 187 MET cc_start: 0.8868 (ttp) cc_final: 0.8628 (ttm) REVERT: A 190 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.5715 (m-70) REVERT: B 82 MET cc_start: 0.6784 (mmm) cc_final: 0.5915 (ptp) REVERT: B 202 MET cc_start: 0.8086 (tpp) cc_final: 0.7848 (tpp) REVERT: B 248 LEU cc_start: 0.8531 (mt) cc_final: 0.7688 (mp) REVERT: C 82 MET cc_start: 0.6948 (pmm) cc_final: 0.6359 (ptt) REVERT: C 115 MET cc_start: 0.7150 (mmt) cc_final: 0.6941 (tpp) REVERT: C 158 PHE cc_start: 0.8225 (m-80) cc_final: 0.7974 (m-10) REVERT: C 202 MET cc_start: 0.8431 (tpp) cc_final: 0.7743 (tpt) REVERT: D 82 MET cc_start: 0.6382 (pmm) cc_final: 0.6159 (pmm) REVERT: E 130 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7911 (tpp-160) REVERT: E 177 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8873 (mp) outliers start: 45 outliers final: 38 residues processed: 180 average time/residue: 0.1073 time to fit residues: 27.4996 Evaluate side-chains 169 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 212 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 37 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 76 ASN B 144 HIS B 190 HIS C 23 GLN C 190 HIS E 85 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.090269 restraints weight = 18249.875| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.46 r_work: 0.3009 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10850 Z= 0.125 Angle : 0.574 7.142 14675 Z= 0.276 Chirality : 0.045 0.141 1610 Planarity : 0.003 0.034 1850 Dihedral : 10.487 105.342 1516 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.19 % Allowed : 12.23 % Favored : 83.58 % 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: -2.34 (0.22), residues: 1325 helix: -1.95 (0.29), residues: 265 sheet: -1.09 (0.25), residues: 385 loop : -1.59 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 130 TYR 0.025 0.001 TYR E 256 PHE 0.010 0.001 PHE D 158 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00288 (10850) covalent geometry : angle 0.57398 (14675) hydrogen bonds : bond 0.02532 ( 327) hydrogen bonds : angle 4.89150 ( 756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4055 (OUTLIER) cc_final: 0.2360 (mt-10) REVERT: A 187 MET cc_start: 0.8850 (ttp) cc_final: 0.8606 (ttm) REVERT: A 190 HIS cc_start: 0.6967 (OUTLIER) cc_final: 0.5697 (m-70) REVERT: B 82 MET cc_start: 0.6697 (mmm) cc_final: 0.5955 (ptp) REVERT: C 115 MET cc_start: 0.7250 (mmt) cc_final: 0.6975 (tpp) REVERT: C 158 PHE cc_start: 0.8229 (m-80) cc_final: 0.7935 (m-10) REVERT: C 202 MET cc_start: 0.8435 (tpp) cc_final: 0.7736 (tpt) REVERT: D 82 MET cc_start: 0.6629 (pmm) cc_final: 0.6238 (pmm) REVERT: D 85 GLN cc_start: 0.8693 (mt0) cc_final: 0.8074 (mp10) REVERT: D 151 GLU cc_start: 0.7829 (tt0) cc_final: 0.7585 (tt0) REVERT: E 124 GLN cc_start: 0.7295 (pt0) cc_final: 0.7023 (pt0) REVERT: E 130 ARG cc_start: 0.8127 (tpp-160) cc_final: 0.7793 (tpp-160) REVERT: E 177 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8887 (mp) outliers start: 48 outliers final: 37 residues processed: 180 average time/residue: 0.1030 time to fit residues: 26.7654 Evaluate side-chains 172 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 85 GLN B 144 HIS B 190 HIS C 190 HIS D 190 HIS E 85 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.106190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.087306 restraints weight = 18529.092| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.46 r_work: 0.2962 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10850 Z= 0.204 Angle : 0.626 7.684 14675 Z= 0.304 Chirality : 0.047 0.156 1610 Planarity : 0.004 0.037 1850 Dihedral : 10.643 111.611 1516 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.45 % Allowed : 12.84 % Favored : 82.71 % 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: -2.32 (0.22), residues: 1325 helix: -1.99 (0.28), residues: 275 sheet: -1.07 (0.25), residues: 385 loop : -1.54 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 130 TYR 0.022 0.002 TYR B 56 PHE 0.015 0.002 PHE D 158 HIS 0.008 0.002 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00476 (10850) covalent geometry : angle 0.62568 (14675) hydrogen bonds : bond 0.02809 ( 327) hydrogen bonds : angle 4.94348 ( 756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 136 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4273 (OUTLIER) cc_final: 0.2286 (mt-10) REVERT: A 187 MET cc_start: 0.8917 (ttp) cc_final: 0.8710 (ttm) REVERT: A 190 HIS cc_start: 0.7319 (OUTLIER) cc_final: 0.5937 (m-70) REVERT: B 82 MET cc_start: 0.7128 (mmm) cc_final: 0.6320 (ptp) REVERT: C 82 MET cc_start: 0.7764 (ptm) cc_final: 0.7563 (ptt) REVERT: C 158 PHE cc_start: 0.8341 (m-80) cc_final: 0.7979 (m-10) REVERT: C 202 MET cc_start: 0.8448 (tpp) cc_final: 0.8058 (tpp) REVERT: D 82 MET cc_start: 0.6660 (pmm) cc_final: 0.5384 (ptt) REVERT: D 85 GLN cc_start: 0.8738 (mt0) cc_final: 0.8114 (mp10) REVERT: E 124 GLN cc_start: 0.7351 (pt0) cc_final: 0.7106 (pt0) REVERT: E 130 ARG cc_start: 0.8216 (tpp-160) cc_final: 0.7894 (tpp-160) REVERT: E 177 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8870 (mp) outliers start: 51 outliers final: 41 residues processed: 174 average time/residue: 0.1012 time to fit residues: 25.3804 Evaluate side-chains 175 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 212 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 33 optimal weight: 0.0470 chunk 91 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 190 HIS E 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.090807 restraints weight = 18280.061| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.45 r_work: 0.2999 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10850 Z= 0.109 Angle : 0.567 6.973 14675 Z= 0.273 Chirality : 0.045 0.127 1610 Planarity : 0.003 0.033 1850 Dihedral : 10.031 100.725 1516 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.02 % Allowed : 13.28 % Favored : 82.71 % 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: -2.30 (0.22), residues: 1325 helix: -2.02 (0.27), residues: 295 sheet: -0.91 (0.25), residues: 385 loop : -1.58 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 130 TYR 0.016 0.001 TYR E 256 PHE 0.014 0.001 PHE D 139 HIS 0.007 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00251 (10850) covalent geometry : angle 0.56659 (14675) hydrogen bonds : bond 0.02434 ( 327) hydrogen bonds : angle 4.70356 ( 756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8935 (ttp) cc_final: 0.8716 (ttm) REVERT: A 190 HIS cc_start: 0.6847 (OUTLIER) cc_final: 0.5593 (m-70) REVERT: B 82 MET cc_start: 0.7119 (mmm) cc_final: 0.6332 (ptp) REVERT: C 115 MET cc_start: 0.7084 (mmt) cc_final: 0.6871 (tpp) REVERT: C 158 PHE cc_start: 0.8283 (m-80) cc_final: 0.7995 (m-10) REVERT: C 202 MET cc_start: 0.8373 (tpp) cc_final: 0.7991 (tpp) REVERT: D 82 MET cc_start: 0.6741 (pmm) cc_final: 0.6235 (pmm) REVERT: D 85 GLN cc_start: 0.8694 (mt0) cc_final: 0.8162 (mp10) REVERT: E 47 ARG cc_start: 0.8746 (ttt180) cc_final: 0.8481 (ttt-90) REVERT: E 124 GLN cc_start: 0.7309 (pt0) cc_final: 0.7046 (pt0) REVERT: E 130 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7851 (tpp-160) REVERT: E 177 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8870 (mp) outliers start: 46 outliers final: 38 residues processed: 178 average time/residue: 0.1040 time to fit residues: 26.5969 Evaluate side-chains 172 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 HIS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 212 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 124 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 190 HIS E 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.088670 restraints weight = 18421.248| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.44 r_work: 0.2981 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10850 Z= 0.162 Angle : 0.605 9.896 14675 Z= 0.291 Chirality : 0.046 0.134 1610 Planarity : 0.003 0.044 1850 Dihedral : 10.098 105.051 1516 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.28 % Allowed : 13.10 % Favored : 82.62 % 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: -1.91 (0.22), residues: 1325 helix: -1.74 (0.28), residues: 275 sheet: -0.59 (0.24), residues: 425 loop : -1.43 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 130 TYR 0.022 0.001 TYR D 256 PHE 0.014 0.001 PHE D 139 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00376 (10850) covalent geometry : angle 0.60518 (14675) hydrogen bonds : bond 0.02616 ( 327) hydrogen bonds : angle 4.75077 ( 756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 133 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4225 (OUTLIER) cc_final: 0.2372 (mt-10) REVERT: A 187 MET cc_start: 0.8927 (ttp) cc_final: 0.8717 (ttm) REVERT: A 190 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.5576 (m-70) REVERT: B 82 MET cc_start: 0.7440 (mmm) cc_final: 0.6322 (ptp) REVERT: C 115 MET cc_start: 0.7177 (mmt) cc_final: 0.6882 (tpp) REVERT: C 158 PHE cc_start: 0.8339 (m-80) cc_final: 0.7995 (m-10) REVERT: C 202 MET cc_start: 0.8330 (tpp) cc_final: 0.8015 (tpp) REVERT: D 46 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8166 (mt-10) REVERT: D 82 MET cc_start: 0.6773 (pmm) cc_final: 0.5445 (ptt) REVERT: D 85 GLN cc_start: 0.8731 (mt0) cc_final: 0.8182 (mp10) REVERT: E 47 ARG cc_start: 0.8797 (ttt180) cc_final: 0.8469 (ttt-90) REVERT: E 124 GLN cc_start: 0.7488 (pt0) cc_final: 0.7218 (pt0) REVERT: E 130 ARG cc_start: 0.8200 (tpp-160) cc_final: 0.7868 (tpp-160) REVERT: E 177 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8841 (mp) outliers start: 49 outliers final: 41 residues processed: 167 average time/residue: 0.0975 time to fit residues: 23.3323 Evaluate side-chains 168 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 HIS Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 243 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 114 optimal weight: 0.0570 chunk 33 optimal weight: 0.4980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS B 23 GLN B 144 HIS B 190 HIS E 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.092208 restraints weight = 18162.016| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.42 r_work: 0.3022 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10850 Z= 0.106 Angle : 0.581 12.985 14675 Z= 0.276 Chirality : 0.044 0.125 1610 Planarity : 0.003 0.033 1850 Dihedral : 9.650 97.808 1516 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.10 % Allowed : 13.89 % Favored : 82.01 % 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: -1.94 (0.22), residues: 1325 helix: -1.75 (0.27), residues: 305 sheet: -0.47 (0.25), residues: 425 loop : -1.53 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 130 TYR 0.018 0.001 TYR D 256 PHE 0.010 0.001 PHE D 158 HIS 0.009 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00243 (10850) covalent geometry : angle 0.58100 (14675) hydrogen bonds : bond 0.02369 ( 327) hydrogen bonds : angle 4.57391 ( 756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8184 (p90) cc_final: 0.7969 (p90) REVERT: A 40 GLU cc_start: 0.3677 (OUTLIER) cc_final: 0.1547 (mt-10) REVERT: A 82 MET cc_start: 0.6925 (mmt) cc_final: 0.5127 (ptp) REVERT: A 187 MET cc_start: 0.8860 (ttp) cc_final: 0.8656 (ttm) REVERT: A 190 HIS cc_start: 0.6664 (OUTLIER) cc_final: 0.5487 (m-70) REVERT: B 82 MET cc_start: 0.7404 (mmm) cc_final: 0.6355 (ptp) REVERT: B 248 LEU cc_start: 0.8609 (mt) cc_final: 0.7638 (mp) REVERT: C 115 MET cc_start: 0.7465 (mmt) cc_final: 0.7228 (tpp) REVERT: C 158 PHE cc_start: 0.8319 (m-80) cc_final: 0.8016 (m-10) REVERT: C 202 MET cc_start: 0.8392 (tpp) cc_final: 0.8018 (tpp) REVERT: D 82 MET cc_start: 0.6897 (pmm) cc_final: 0.5620 (ptt) REVERT: D 85 GLN cc_start: 0.8708 (mt0) cc_final: 0.8156 (mp10) REVERT: E 47 ARG cc_start: 0.8725 (ttt180) cc_final: 0.8405 (ttt-90) REVERT: E 124 GLN cc_start: 0.7517 (pt0) cc_final: 0.7263 (pt0) REVERT: E 130 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7866 (tpp-160) REVERT: E 177 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8849 (mp) outliers start: 47 outliers final: 36 residues processed: 175 average time/residue: 0.0960 time to fit residues: 24.6211 Evaluate side-chains 178 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 HIS Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN B 23 GLN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS E 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.090931 restraints weight = 18201.262| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.31 r_work: 0.3002 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10850 Z= 0.129 Angle : 0.603 11.559 14675 Z= 0.286 Chirality : 0.045 0.130 1610 Planarity : 0.003 0.032 1850 Dihedral : 9.603 99.962 1516 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.19 % Allowed : 14.41 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.87 (0.22), residues: 1325 helix: -1.63 (0.27), residues: 305 sheet: -0.43 (0.25), residues: 425 loop : -1.53 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 130 TYR 0.023 0.001 TYR D 256 PHE 0.012 0.001 PHE D 158 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00299 (10850) covalent geometry : angle 0.60288 (14675) hydrogen bonds : bond 0.02441 ( 327) hydrogen bonds : angle 4.58167 ( 756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4051 (OUTLIER) cc_final: 0.1991 (mt-10) REVERT: A 82 MET cc_start: 0.7272 (mmt) cc_final: 0.5332 (ptp) REVERT: A 137 LYS cc_start: 0.7491 (mmmm) cc_final: 0.7260 (pttt) REVERT: A 187 MET cc_start: 0.9071 (ttp) cc_final: 0.8851 (ttm) REVERT: A 190 HIS cc_start: 0.6957 (OUTLIER) cc_final: 0.5802 (m-70) REVERT: B 82 MET cc_start: 0.7569 (mmm) cc_final: 0.6477 (ptt) REVERT: B 190 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.6523 (m90) REVERT: C 115 MET cc_start: 0.7549 (mmt) cc_final: 0.7257 (tpp) REVERT: C 158 PHE cc_start: 0.8431 (m-80) cc_final: 0.8063 (m-10) REVERT: C 202 MET cc_start: 0.8443 (tpp) cc_final: 0.8125 (tpp) REVERT: D 82 MET cc_start: 0.6963 (pmm) cc_final: 0.5706 (ptt) REVERT: D 85 GLN cc_start: 0.8836 (mt0) cc_final: 0.8282 (mp10) REVERT: E 47 ARG cc_start: 0.8800 (ttt180) cc_final: 0.8503 (ttt-90) REVERT: E 124 GLN cc_start: 0.7573 (pt0) cc_final: 0.7293 (pt0) REVERT: E 130 ARG cc_start: 0.8267 (tpp-160) cc_final: 0.7919 (tpp-160) REVERT: E 177 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8879 (mp) outliers start: 48 outliers final: 40 residues processed: 163 average time/residue: 0.0953 time to fit residues: 22.5755 Evaluate side-chains 171 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 HIS Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 10 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 118 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS B 190 HIS E 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.092179 restraints weight = 18236.356| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.32 r_work: 0.3021 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10850 Z= 0.111 Angle : 0.582 10.906 14675 Z= 0.278 Chirality : 0.044 0.126 1610 Planarity : 0.003 0.033 1850 Dihedral : 9.398 99.892 1516 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.76 % Allowed : 14.76 % Favored : 81.48 % 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: -1.80 (0.22), residues: 1325 helix: -1.53 (0.28), residues: 305 sheet: -0.39 (0.25), residues: 425 loop : -1.51 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 130 TYR 0.025 0.001 TYR E 56 PHE 0.013 0.001 PHE D 158 HIS 0.003 0.001 HIS D 81 Details of bonding type rmsd covalent geometry : bond 0.00254 (10850) covalent geometry : angle 0.58228 (14675) hydrogen bonds : bond 0.02372 ( 327) hydrogen bonds : angle 4.50728 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2120.98 seconds wall clock time: 37 minutes 24.94 seconds (2244.94 seconds total)