Starting phenix.real_space_refine on Mon Jul 28 22:05:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6f95_4196/07_2025/6f95_4196.cif Found real_map, /net/cci-nas-00/data/ceres_data/6f95_4196/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6f95_4196/07_2025/6f95_4196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6f95_4196/07_2025/6f95_4196.map" model { file = "/net/cci-nas-00/data/ceres_data/6f95_4196/07_2025/6f95_4196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6f95_4196/07_2025/6f95_4196.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.65, per 1000 atoms: 0.72 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: 2.87 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.46 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: 3.91 Time building geometry restraints manager: 3.43 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 57.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.530 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.240 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.005 0.002 HIS D 81 PHE 0.028 0.003 PHE C 126 TYR 0.032 0.003 TYR A 56 ARG 0.006 0.001 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.27283 ( 327) hydrogen bonds : angle 9.93962 ( 756) covalent geometry : bond 0.00733 (10850) covalent geometry : angle 0.89374 (14675) *********************** 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 : 1.171 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: 0.8548 (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 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: 0.2358 time to fit residues: 112.4573 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 : 1.210 ------------------------------------------------------------------------------- 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 109 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 144 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 76 ASN C 125 HIS C 190 HIS D 11 ASN D 125 HIS E 11 ASN E 76 ASN E 85 GLN E 125 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.091389 restraints weight = 18027.975| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.43 r_work: 0.3032 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10850 Z= 0.181 Angle : 0.669 7.757 14675 Z= 0.327 Chirality : 0.047 0.136 1610 Planarity : 0.005 0.044 1850 Dihedral : 11.656 112.371 1517 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.23 % Allowed : 8.56 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.21), residues: 1325 helix: -3.34 (0.22), residues: 250 sheet: -1.73 (0.25), residues: 385 loop : -1.73 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 190 PHE 0.012 0.002 PHE E 158 TYR 0.017 0.002 TYR C 56 ARG 0.006 0.001 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 327) hydrogen bonds : angle 5.82453 ( 756) covalent geometry : bond 0.00415 (10850) covalent geometry : angle 0.66865 (14675) *********************** 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 228 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 60 THR cc_start: 0.9353 (p) cc_final: 0.9139 (p) REVERT: A 82 MET cc_start: 0.7128 (mmm) cc_final: 0.6092 (pmm) REVERT: B 82 MET cc_start: 0.6558 (mmm) cc_final: 0.5895 (pmm) REVERT: B 202 MET cc_start: 0.8042 (tpp) cc_final: 0.7719 (tpp) REVERT: B 206 LYS cc_start: 0.8671 (mttt) cc_final: 0.8372 (mtmm) REVERT: B 248 LEU cc_start: 0.8423 (mt) cc_final: 0.7881 (mt) REVERT: C 115 MET cc_start: 0.7050 (mmt) cc_final: 0.6821 (tpp) REVERT: C 187 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7840 (ttt) REVERT: C 202 MET cc_start: 0.8581 (tpp) cc_final: 0.8256 (tpp) REVERT: C 254 SER cc_start: 0.8563 (m) cc_final: 0.8219 (t) REVERT: D 82 MET cc_start: 0.6992 (mmm) cc_final: 0.6605 (ptt) REVERT: D 186 LYS cc_start: 0.8805 (ttmt) cc_final: 0.8604 (tptt) REVERT: D 256 TYR cc_start: 0.8692 (m-80) cc_final: 0.8132 (m-80) outliers start: 37 outliers final: 24 residues processed: 221 average time/residue: 0.2317 time to fit residues: 71.6886 Evaluate side-chains 162 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 177 LEU 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 B residue 259 SER 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 187 MET 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 166 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 243 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 Chi-restraints excluded: chain E residue 190 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 23 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.0470 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN C 190 HIS E 85 GLN E 124 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.086951 restraints weight = 18617.520| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.45 r_work: 0.2956 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10850 Z= 0.235 Angle : 0.675 7.394 14675 Z= 0.332 Chirality : 0.048 0.154 1610 Planarity : 0.004 0.043 1850 Dihedral : 11.576 117.979 1516 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.28 % Allowed : 10.57 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.21), residues: 1325 helix: -2.57 (0.26), residues: 260 sheet: -1.54 (0.25), residues: 385 loop : -1.63 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 190 PHE 0.015 0.002 PHE D 158 TYR 0.020 0.002 TYR C 56 ARG 0.006 0.001 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 327) hydrogen bonds : angle 5.50791 ( 756) covalent geometry : bond 0.00546 (10850) covalent geometry : angle 0.67524 (14675) *********************** 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: 49 poor density : 154 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4512 (OUTLIER) cc_final: 0.2857 (mt-10) REVERT: A 190 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.6046 (m-70) REVERT: B 82 MET cc_start: 0.6715 (mmm) cc_final: 0.6042 (pmm) REVERT: B 202 MET cc_start: 0.8172 (tpp) cc_final: 0.7900 (tpp) REVERT: B 233 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8363 (mm-30) REVERT: B 248 LEU cc_start: 0.8569 (mt) cc_final: 0.7760 (mp) REVERT: C 82 MET cc_start: 0.7054 (pmm) cc_final: 0.6136 (ptm) REVERT: C 187 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7926 (ttt) REVERT: C 202 MET cc_start: 0.8508 (tpp) cc_final: 0.8055 (tpp) REVERT: C 254 SER cc_start: 0.8523 (m) cc_final: 0.8317 (p) REVERT: D 46 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8090 (mt-10) REVERT: D 82 MET cc_start: 0.7099 (mmm) cc_final: 0.6687 (ptt) REVERT: E 130 ARG cc_start: 0.8109 (tpp-160) cc_final: 0.7888 (tpp-160) outliers start: 49 outliers final: 34 residues processed: 190 average time/residue: 0.2474 time to fit residues: 65.8116 Evaluate side-chains 156 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 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 24 ILE 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 198 ASP 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 134 VAL Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 187 MET 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 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 4 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 70 optimal weight: 0.0980 chunk 47 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 37 optimal weight: 0.0060 chunk 51 optimal weight: 0.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 HIS C 190 HIS E 85 GLN E 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.092305 restraints weight = 17946.230| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.43 r_work: 0.3043 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10850 Z= 0.102 Angle : 0.576 7.064 14675 Z= 0.277 Chirality : 0.045 0.150 1610 Planarity : 0.003 0.035 1850 Dihedral : 10.516 107.017 1516 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.14 % Allowed : 12.31 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.21), residues: 1325 helix: -2.06 (0.28), residues: 260 sheet: -1.20 (0.26), residues: 385 loop : -1.69 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 81 PHE 0.010 0.001 PHE E 141 TYR 0.014 0.001 TYR C 256 ARG 0.007 0.001 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.02495 ( 327) hydrogen bonds : angle 4.97211 ( 756) covalent geometry : bond 0.00226 (10850) covalent geometry : angle 0.57583 (14675) *********************** 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 198 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4023 (OUTLIER) cc_final: 0.2096 (mt-10) REVERT: A 82 MET cc_start: 0.7299 (mmm) cc_final: 0.5503 (pmm) REVERT: A 190 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.5437 (m-70) REVERT: B 82 MET cc_start: 0.6565 (mmm) cc_final: 0.6064 (pmm) REVERT: B 233 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8302 (mm-30) REVERT: C 82 MET cc_start: 0.6870 (pmm) cc_final: 0.6445 (ptm) REVERT: C 158 PHE cc_start: 0.8188 (m-80) cc_final: 0.7924 (m-10) REVERT: C 187 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7924 (ttt) REVERT: C 202 MET cc_start: 0.8452 (tpp) cc_final: 0.7967 (tpp) REVERT: D 82 MET cc_start: 0.7099 (mmm) cc_final: 0.6749 (pmm) REVERT: D 85 GLN cc_start: 0.8634 (mt0) cc_final: 0.8098 (mp10) REVERT: D 106 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8834 (mp) REVERT: E 42 TYR cc_start: 0.7836 (p90) cc_final: 0.7632 (p90) REVERT: E 151 GLU cc_start: 0.8314 (tt0) cc_final: 0.8085 (mt-10) outliers start: 36 outliers final: 24 residues processed: 185 average time/residue: 0.2368 time to fit residues: 62.8472 Evaluate side-chains 166 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 247 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 26 VAL 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 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 187 MET Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 248 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 4 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN C 23 GLN C 190 HIS D 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 = 0.3402 r_free = 0.3402 target = 0.108983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.090266 restraints weight = 18084.183| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.45 r_work: 0.3004 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10850 Z= 0.135 Angle : 0.582 7.162 14675 Z= 0.280 Chirality : 0.045 0.144 1610 Planarity : 0.003 0.033 1850 Dihedral : 10.317 104.496 1516 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.37 % Allowed : 12.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.21), residues: 1325 helix: -2.13 (0.27), residues: 295 sheet: -1.04 (0.25), residues: 385 loop : -1.74 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 81 PHE 0.010 0.001 PHE D 158 TYR 0.017 0.001 TYR D 256 ARG 0.004 0.001 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.02547 ( 327) hydrogen bonds : angle 4.82800 ( 756) covalent geometry : bond 0.00310 (10850) covalent geometry : angle 0.58157 (14675) *********************** 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 197 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4229 (OUTLIER) cc_final: 0.2382 (mt-10) REVERT: A 82 MET cc_start: 0.7333 (mmm) cc_final: 0.7040 (mmm) REVERT: A 190 HIS cc_start: 0.6929 (OUTLIER) cc_final: 0.5645 (m-70) REVERT: B 82 MET cc_start: 0.6769 (mmm) cc_final: 0.6102 (ptp) REVERT: B 233 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8328 (mm-30) REVERT: C 148 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.7000 (mtt) REVERT: C 158 PHE cc_start: 0.8271 (m-80) cc_final: 0.7900 (m-10) REVERT: C 187 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7947 (ttt) REVERT: D 82 MET cc_start: 0.7226 (mmm) cc_final: 0.6804 (pmm) REVERT: D 85 GLN cc_start: 0.8731 (mt0) cc_final: 0.8151 (mp10) outliers start: 50 outliers final: 37 residues processed: 180 average time/residue: 0.2207 time to fit residues: 57.2404 Evaluate side-chains 174 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 144 HIS Chi-restraints excluded: chain A residue 177 LEU 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 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 187 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 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 222 VAL 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 190 HIS Chi-restraints excluded: chain E residue 212 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 46 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 103 optimal weight: 0.0370 chunk 92 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.4662 ------------------------------------------------------------------------------- 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 85 GLN D 190 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.088136 restraints weight = 18423.747| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.47 r_work: 0.2971 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10850 Z= 0.178 Angle : 0.609 7.640 14675 Z= 0.295 Chirality : 0.046 0.146 1610 Planarity : 0.003 0.039 1850 Dihedral : 10.333 107.641 1516 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.54 % Allowed : 12.14 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.22), residues: 1325 helix: -1.87 (0.28), residues: 275 sheet: -0.97 (0.26), residues: 385 loop : -1.53 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 81 PHE 0.013 0.001 PHE D 158 TYR 0.019 0.002 TYR D 256 ARG 0.006 0.001 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.02700 ( 327) hydrogen bonds : angle 4.83667 ( 756) covalent geometry : bond 0.00413 (10850) covalent geometry : angle 0.60936 (14675) *********************** 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 191 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 139 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4222 (OUTLIER) cc_final: 0.2374 (mt-10) REVERT: A 87 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7500 (mtm-85) REVERT: A 190 HIS cc_start: 0.7182 (OUTLIER) cc_final: 0.5728 (m-70) REVERT: B 82 MET cc_start: 0.7179 (mmm) cc_final: 0.6365 (ptp) REVERT: B 233 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8340 (mm-30) REVERT: C 148 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.7053 (mtt) REVERT: C 158 PHE cc_start: 0.8330 (m-80) cc_final: 0.8010 (m-10) REVERT: C 187 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7985 (ttt) REVERT: C 202 MET cc_start: 0.8320 (tpp) cc_final: 0.7853 (tpp) REVERT: D 82 MET cc_start: 0.7319 (mmm) cc_final: 0.6752 (ptt) REVERT: D 85 GLN cc_start: 0.8749 (mt0) cc_final: 0.8147 (mp10) REVERT: D 148 MET cc_start: 0.7484 (ttt) cc_final: 0.7139 (mtp) REVERT: E 47 ARG cc_start: 0.8799 (ttt180) cc_final: 0.8500 (ttt-90) REVERT: E 124 GLN cc_start: 0.7110 (pt0) cc_final: 0.6900 (pt0) REVERT: E 130 ARG cc_start: 0.8046 (ttm110) cc_final: 0.7751 (ttm110) outliers start: 52 outliers final: 41 residues processed: 174 average time/residue: 0.2312 time to fit residues: 56.6386 Evaluate side-chains 175 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 87 ARG 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 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 B residue 265 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 81 HIS 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 187 MET Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 212 CYS 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 166 ILE 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 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 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 9 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 7 optimal weight: 0.0670 chunk 101 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 11 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: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.091759 restraints weight = 18385.129| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.42 r_work: 0.3029 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10850 Z= 0.110 Angle : 0.561 6.664 14675 Z= 0.270 Chirality : 0.044 0.143 1610 Planarity : 0.003 0.033 1850 Dihedral : 9.744 100.189 1516 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.10 % Allowed : 12.23 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.22), residues: 1325 helix: -1.96 (0.26), residues: 315 sheet: -0.60 (0.25), residues: 425 loop : -1.59 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 81 PHE 0.008 0.001 PHE A 29 TYR 0.021 0.001 TYR E 256 ARG 0.008 0.001 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.02366 ( 327) hydrogen bonds : angle 4.62009 ( 756) covalent geometry : bond 0.00253 (10850) covalent geometry : angle 0.56082 (14675) *********************** 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: 47 poor density : 147 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.3765 (OUTLIER) cc_final: 0.2042 (mt-10) REVERT: A 82 MET cc_start: 0.7153 (mmt) cc_final: 0.5325 (ptp) REVERT: A 190 HIS cc_start: 0.6662 (OUTLIER) cc_final: 0.5424 (m-70) REVERT: A 202 MET cc_start: 0.7253 (tpp) cc_final: 0.7002 (tpt) REVERT: B 82 MET cc_start: 0.7236 (mmm) cc_final: 0.6356 (ptp) REVERT: B 233 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8206 (mm-30) REVERT: C 148 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7033 (mtt) REVERT: C 158 PHE cc_start: 0.8300 (m-80) cc_final: 0.8034 (m-10) REVERT: C 187 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7897 (ttt) REVERT: C 202 MET cc_start: 0.8344 (tpp) cc_final: 0.8096 (tpp) REVERT: D 82 MET cc_start: 0.7407 (mmm) cc_final: 0.6907 (ptt) REVERT: D 85 GLN cc_start: 0.8702 (mt0) cc_final: 0.8166 (mp10) REVERT: D 148 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6732 (mtp) REVERT: E 47 ARG cc_start: 0.8755 (ttt180) cc_final: 0.8499 (ttt-90) REVERT: E 130 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7758 (ttm170) outliers start: 47 outliers final: 36 residues processed: 174 average time/residue: 0.2531 time to fit residues: 63.6124 Evaluate side-chains 174 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 177 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 26 VAL Chi-restraints excluded: chain B residue 45 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 82 MET 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 148 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 212 CYS 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 148 MET Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 248 LEU 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 190 HIS Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 243 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 54 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 72 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** A 199 ASN B 23 GLN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.091333 restraints weight = 18119.657| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.38 r_work: 0.3010 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10850 Z= 0.116 Angle : 0.571 7.942 14675 Z= 0.274 Chirality : 0.044 0.140 1610 Planarity : 0.003 0.033 1850 Dihedral : 9.555 98.710 1516 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.45 % Allowed : 12.23 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.22), residues: 1325 helix: -1.81 (0.26), residues: 315 sheet: -0.49 (0.25), residues: 425 loop : -1.58 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 81 PHE 0.008 0.001 PHE D 158 TYR 0.023 0.001 TYR E 256 ARG 0.008 0.001 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.02323 ( 327) hydrogen bonds : angle 4.53356 ( 756) covalent geometry : bond 0.00266 (10850) covalent geometry : angle 0.57080 (14675) *********************** 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 195 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.3838 (OUTLIER) cc_final: 0.2053 (mt-10) REVERT: A 82 MET cc_start: 0.7095 (mmt) cc_final: 0.5487 (ptp) REVERT: A 190 HIS cc_start: 0.6598 (OUTLIER) cc_final: 0.5348 (m-70) REVERT: A 202 MET cc_start: 0.7232 (tpp) cc_final: 0.7009 (tpt) REVERT: B 82 MET cc_start: 0.7390 (mmm) cc_final: 0.6343 (ptp) REVERT: B 233 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8326 (mm-30) REVERT: B 248 LEU cc_start: 0.8584 (mt) cc_final: 0.7624 (mp) REVERT: C 148 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.7024 (mtt) REVERT: C 158 PHE cc_start: 0.8319 (m-80) cc_final: 0.8029 (m-10) REVERT: C 187 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7919 (ttt) REVERT: C 202 MET cc_start: 0.8357 (tpp) cc_final: 0.8121 (tpp) REVERT: D 82 MET cc_start: 0.7503 (mmm) cc_final: 0.6938 (ptt) REVERT: D 85 GLN cc_start: 0.8698 (mt0) cc_final: 0.8151 (mp10) REVERT: E 47 ARG cc_start: 0.8755 (ttt180) cc_final: 0.8503 (ttt-90) outliers start: 51 outliers final: 36 residues processed: 175 average time/residue: 0.2971 time to fit residues: 75.9612 Evaluate side-chains 170 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 177 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 26 VAL Chi-restraints excluded: chain B residue 45 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 148 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 212 CYS 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 190 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 248 LEU 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 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 37 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 126 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 81 HIS B 85 GLN E 81 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.087815 restraints weight = 18491.703| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.40 r_work: 0.2971 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10850 Z= 0.218 Angle : 0.648 7.135 14675 Z= 0.316 Chirality : 0.047 0.155 1610 Planarity : 0.004 0.066 1850 Dihedral : 10.040 102.088 1516 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 4.54 % Allowed : 12.49 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.22), residues: 1325 helix: -1.66 (0.27), residues: 290 sheet: -0.56 (0.25), residues: 425 loop : -1.42 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 81 PHE 0.021 0.002 PHE D 126 TYR 0.025 0.002 TYR D 256 ARG 0.008 0.001 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.02775 ( 327) hydrogen bonds : angle 4.78177 ( 756) covalent geometry : bond 0.00506 (10850) covalent geometry : angle 0.64766 (14675) *********************** 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 183 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4617 (OUTLIER) cc_final: 0.2557 (mt-10) REVERT: A 190 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.5878 (m-70) REVERT: B 82 MET cc_start: 0.7543 (mmm) cc_final: 0.6396 (ptt) REVERT: B 87 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7812 (mtm-85) REVERT: B 233 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8382 (mm-30) REVERT: C 158 PHE cc_start: 0.8433 (m-80) cc_final: 0.8039 (m-10) REVERT: C 187 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7992 (ttt) REVERT: C 202 MET cc_start: 0.8359 (tpp) cc_final: 0.7935 (tpp) REVERT: D 82 MET cc_start: 0.7519 (mmm) cc_final: 0.6960 (ptt) REVERT: D 85 GLN cc_start: 0.8757 (mt0) cc_final: 0.8199 (mp10) REVERT: D 256 TYR cc_start: 0.8775 (m-80) cc_final: 0.8458 (m-80) REVERT: E 47 ARG cc_start: 0.8822 (ttt180) cc_final: 0.8449 (ttt-90) outliers start: 52 outliers final: 42 residues processed: 163 average time/residue: 0.3167 time to fit residues: 73.8526 Evaluate side-chains 171 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 85 GLN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 190 HIS 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 87 ARG 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 B residue 265 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 82 MET 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 187 MET Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 212 CYS 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 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 222 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 4 THR 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 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 17 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.108641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.090401 restraints weight = 18175.662| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.37 r_work: 0.2990 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5194 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= 0.134 Angle : 0.611 14.191 14675 Z= 0.292 Chirality : 0.045 0.139 1610 Planarity : 0.003 0.039 1850 Dihedral : 9.742 99.980 1516 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.76 % Allowed : 13.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.22), residues: 1325 helix: -1.50 (0.28), residues: 280 sheet: -0.48 (0.25), residues: 425 loop : -1.46 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 81 PHE 0.014 0.001 PHE D 126 TYR 0.023 0.001 TYR E 56 ARG 0.010 0.001 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.02519 ( 327) hydrogen bonds : angle 4.65407 ( 756) covalent geometry : bond 0.00312 (10850) covalent geometry : angle 0.61150 (14675) ********************** 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 177 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4116 (OUTLIER) cc_final: 0.1822 (mp0) REVERT: A 82 MET cc_start: 0.7206 (mmt) cc_final: 0.5379 (ptp) REVERT: A 190 HIS cc_start: 0.6882 (OUTLIER) cc_final: 0.5447 (m-70) REVERT: B 82 MET cc_start: 0.7572 (mmm) cc_final: 0.6468 (ptp) REVERT: B 233 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8312 (mm-30) REVERT: C 187 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7964 (ttt) REVERT: C 202 MET cc_start: 0.8324 (tpp) cc_final: 0.8035 (tpp) REVERT: D 82 MET cc_start: 0.7534 (mmm) cc_final: 0.6962 (ptt) REVERT: D 85 GLN cc_start: 0.8709 (mt0) cc_final: 0.8186 (mp10) REVERT: D 256 TYR cc_start: 0.8767 (m-80) cc_final: 0.8338 (m-10) REVERT: E 47 ARG cc_start: 0.8780 (ttt180) cc_final: 0.8468 (ttt-90) outliers start: 43 outliers final: 39 residues processed: 160 average time/residue: 0.2227 time to fit residues: 50.6385 Evaluate side-chains 167 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 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 B residue 265 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 82 MET 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 187 MET Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 212 CYS 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 190 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 248 LEU 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 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 57 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 0.0770 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN E 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.092524 restraints weight = 18081.304| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.32 r_work: 0.3054 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10850 Z= 0.106 Angle : 0.585 12.584 14675 Z= 0.277 Chirality : 0.044 0.138 1610 Planarity : 0.003 0.044 1850 Dihedral : 9.303 97.846 1516 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.84 % Allowed : 13.80 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.22), residues: 1325 helix: -1.53 (0.27), residues: 315 sheet: -0.38 (0.25), residues: 425 loop : -1.48 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 81 PHE 0.012 0.001 PHE D 126 TYR 0.022 0.001 TYR E 256 ARG 0.008 0.001 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.02316 ( 327) hydrogen bonds : angle 4.49160 ( 756) covalent geometry : bond 0.00239 (10850) covalent geometry : angle 0.58494 (14675) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4410.99 seconds wall clock time: 79 minutes 39.54 seconds (4779.54 seconds total)