Starting phenix.real_space_refine on Fri Feb 14 22:44:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6f95_4196/02_2025/6f95_4196.cif Found real_map, /net/cci-nas-00/data/ceres_data/6f95_4196/02_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_4196/02_2025/6f95_4196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6f95_4196/02_2025/6f95_4196.map" model { file = "/net/cci-nas-00/data/ceres_data/6f95_4196/02_2025/6f95_4196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6f95_4196/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.55, per 1000 atoms: 0.62 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: 2.70 Conformation dependent library (CDL) restraints added in 1.2 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: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 60 through 66 removed outlier: 3.885A pdb=" N PHE A 66 " --> pdb=" O ASN A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.866A pdb=" N MET A 72 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.948A pdb=" N LEU A 88 " --> pdb=" O GLY A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.608A pdb=" N LYS A 120 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.825A pdb=" N ASN A 157 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.829A pdb=" N LYS A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 236 removed outlier: 4.122A pdb=" N GLU A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 256 through 264 removed outlier: 4.252A pdb=" N LEU A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 66 removed outlier: 3.885A pdb=" N PHE B 66 " --> pdb=" O ASN B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 removed outlier: 3.867A pdb=" N MET B 72 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 97 removed outlier: 3.948A pdb=" N LEU B 88 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 removed outlier: 3.607A pdb=" N LYS B 120 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.826A pdb=" N ASN B 157 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 212 removed outlier: 3.830A pdb=" N LYS B 206 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 236 removed outlier: 4.122A pdb=" N GLU B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 256 through 264 removed outlier: 4.253A pdb=" N LEU B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 removed outlier: 3.885A pdb=" N PHE C 66 " --> pdb=" O ASN C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.866A pdb=" N MET C 72 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 97 removed outlier: 3.948A pdb=" N LEU C 88 " --> pdb=" O GLY C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.607A pdb=" N LYS C 120 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.826A pdb=" N ASN C 157 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 212 removed outlier: 3.829A pdb=" N LYS C 206 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 236 removed outlier: 4.121A pdb=" N GLU C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 264 removed outlier: 4.253A pdb=" N LEU C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 66 removed outlier: 3.884A pdb=" N PHE D 66 " --> pdb=" O ASN D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 72 removed outlier: 3.867A pdb=" N MET D 72 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 97 removed outlier: 3.948A pdb=" N LEU D 88 " --> pdb=" O GLY D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 removed outlier: 3.608A pdb=" N LYS D 120 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 159 removed outlier: 3.826A pdb=" N ASN D 157 " --> pdb=" O GLY D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 212 removed outlier: 3.829A pdb=" N LYS D 206 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 236 removed outlier: 4.121A pdb=" N GLU D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 264 removed outlier: 4.253A pdb=" N LEU D 262 " --> pdb=" O ASN D 258 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 66 removed outlier: 3.885A pdb=" N PHE E 66 " --> pdb=" O ASN E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 removed outlier: 3.868A pdb=" N MET E 72 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 97 removed outlier: 3.949A pdb=" N LEU E 88 " --> pdb=" O GLY E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.607A pdb=" N LYS E 120 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 159 removed outlier: 3.826A pdb=" N ASN E 157 " --> pdb=" O GLY E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 212 removed outlier: 3.829A pdb=" N LYS E 206 " --> pdb=" O MET E 202 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS E 210 " --> pdb=" O LYS E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 236 removed outlier: 4.122A pdb=" N GLU E 233 " --> pdb=" O GLU E 229 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS E 234 " --> pdb=" O GLU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 256 through 264 removed outlier: 4.253A pdb=" N LEU E 262 " --> pdb=" O ASN E 258 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 3.848A pdb=" N THR A 109 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE A 9 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS A 144 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU A 106 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE A 146 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 108 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET A 148 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N CYS A 110 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A 150 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS A 34 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 193 removed outlier: 6.382A pdb=" N VAL A 165 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR A 224 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL A 167 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 30 removed outlier: 3.848A pdb=" N THR B 109 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE B 9 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS B 144 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU B 106 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE B 146 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 108 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET B 148 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N CYS B 110 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA B 150 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 34 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 192 through 193 removed outlier: 6.383A pdb=" N VAL B 165 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR B 224 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 167 " --> pdb=" O THR B 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 30 removed outlier: 3.847A pdb=" N THR C 109 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE C 9 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS C 144 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU C 106 " --> pdb=" O HIS C 144 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE C 146 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU C 108 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET C 148 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N CYS C 110 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA C 150 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS C 34 " --> pdb=" O TYR C 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 192 through 193 removed outlier: 6.382A pdb=" N VAL C 165 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR C 224 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL C 167 " --> pdb=" O THR C 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 30 removed outlier: 3.849A pdb=" N THR D 109 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE D 9 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS D 144 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU D 106 " --> pdb=" O HIS D 144 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE D 146 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU D 108 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET D 148 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N CYS D 110 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA D 150 " --> pdb=" O CYS D 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS D 34 " --> pdb=" O TYR D 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 192 through 193 removed outlier: 6.381A pdb=" N VAL D 165 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR D 224 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL D 167 " --> pdb=" O THR D 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 25 through 30 removed outlier: 3.849A pdb=" N THR E 109 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE E 9 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS E 144 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU E 106 " --> pdb=" O HIS E 144 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE E 146 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU E 108 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET E 148 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N CYS E 110 " --> pdb=" O MET E 148 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA E 150 " --> pdb=" O CYS E 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS E 34 " --> pdb=" O TYR E 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 192 through 193 removed outlier: 6.383A pdb=" N VAL E 165 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR E 224 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL E 167 " --> pdb=" O THR E 224 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 3.05 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.370 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.160 ------------------------------------------------------------------------------- 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= 0.475 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 *********************** 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 : 1.191 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: 0.2424 time to fit residues: 115.1382 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 : 1.185 ------------------------------------------------------------------------------- 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 = 18027.965| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.43 r_work: 0.3029 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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= 0.267 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 *********************** 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 : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 60 THR cc_start: 0.9357 (p) cc_final: 0.9140 (p) REVERT: A 82 MET cc_start: 0.7136 (mmm) cc_final: 0.6084 (pmm) REVERT: B 82 MET cc_start: 0.6560 (mmm) cc_final: 0.5891 (pmm) REVERT: B 202 MET cc_start: 0.8033 (tpp) cc_final: 0.7707 (tpp) REVERT: B 206 LYS cc_start: 0.8668 (mttt) cc_final: 0.8364 (mtmm) REVERT: B 248 LEU cc_start: 0.8421 (mt) cc_final: 0.7873 (mt) REVERT: C 115 MET cc_start: 0.7072 (mmt) cc_final: 0.6832 (tpp) REVERT: C 187 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7839 (ttt) REVERT: C 202 MET cc_start: 0.8569 (tpp) cc_final: 0.8243 (tpp) REVERT: C 254 SER cc_start: 0.8564 (m) cc_final: 0.8212 (t) REVERT: D 82 MET cc_start: 0.6987 (mmm) cc_final: 0.6593 (ptt) REVERT: D 186 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8598 (tptt) REVERT: D 256 TYR cc_start: 0.8695 (m-80) cc_final: 0.8127 (m-80) outliers start: 37 outliers final: 24 residues processed: 221 average time/residue: 0.2435 time to fit residues: 74.8371 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 : 1.235 ------------------------------------------------------------------------------- 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: 5.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 120 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 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** 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 = 0.3392 r_free = 0.3392 target = 0.108231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.089370 restraints weight = 18446.396| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.46 r_work: 0.2988 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4044 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= 0.256 Angle : 0.632 7.246 14675 Z= 0.308 Chirality : 0.046 0.154 1610 Planarity : 0.004 0.040 1850 Dihedral : 11.194 111.495 1516 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.76 % Allowed : 10.74 % Favored : 85.50 % 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: -2.67 (0.21), residues: 1325 helix: -2.53 (0.26), residues: 255 sheet: -1.45 (0.25), residues: 385 loop : -1.58 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 81 PHE 0.013 0.001 PHE D 126 TYR 0.015 0.002 TYR C 56 ARG 0.006 0.001 ARG A 130 *********************** 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 205 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4292 (OUTLIER) cc_final: 0.2248 (mt-10) REVERT: A 60 THR cc_start: 0.9376 (p) cc_final: 0.9130 (p) REVERT: A 82 MET cc_start: 0.7016 (mmm) cc_final: 0.6121 (pmm) REVERT: A 190 HIS cc_start: 0.7070 (OUTLIER) cc_final: 0.5643 (m-70) REVERT: B 82 MET cc_start: 0.6610 (mmm) cc_final: 0.5978 (pmm) REVERT: B 202 MET cc_start: 0.8191 (tpp) cc_final: 0.7934 (tpp) REVERT: B 233 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8321 (mm-30) REVERT: B 248 LEU cc_start: 0.8529 (mt) cc_final: 0.7706 (mp) REVERT: C 82 MET cc_start: 0.6982 (pmm) cc_final: 0.6040 (ptm) REVERT: C 187 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7903 (ttt) REVERT: C 202 MET cc_start: 0.8490 (tpp) cc_final: 0.8014 (tpp) REVERT: C 254 SER cc_start: 0.8483 (m) cc_final: 0.8283 (p) REVERT: D 46 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8055 (mt-10) REVERT: D 82 MET cc_start: 0.7103 (mmm) cc_final: 0.6663 (ptt) REVERT: E 130 ARG cc_start: 0.8062 (tpp-160) cc_final: 0.7781 (tpp-160) outliers start: 43 outliers final: 29 residues processed: 190 average time/residue: 0.2338 time to fit residues: 62.5117 Evaluate side-chains 160 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 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 134 VAL 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 222 VAL 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 147 VAL 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: 5.9990 chunk 47 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** C 190 HIS D 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 = 0.3399 r_free = 0.3399 target = 0.108814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.089987 restraints weight = 18109.040| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.45 r_work: 0.2998 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10850 Z= 0.212 Angle : 0.593 7.189 14675 Z= 0.287 Chirality : 0.046 0.161 1610 Planarity : 0.003 0.040 1850 Dihedral : 10.676 106.574 1516 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.93 % Allowed : 11.62 % Favored : 84.45 % 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: -2.46 (0.21), residues: 1325 helix: -2.15 (0.28), residues: 265 sheet: -1.21 (0.25), residues: 385 loop : -1.59 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 190 PHE 0.011 0.001 PHE D 126 TYR 0.015 0.001 TYR B 56 ARG 0.007 0.001 ARG A 130 *********************** 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 193 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4206 (OUTLIER) cc_final: 0.2299 (mt-10) REVERT: A 190 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.5636 (m-70) REVERT: B 82 MET cc_start: 0.6721 (mmm) cc_final: 0.6061 (pmm) REVERT: B 202 MET cc_start: 0.8233 (tpp) cc_final: 0.8024 (tpp) REVERT: B 233 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8317 (mm-30) REVERT: B 248 LEU cc_start: 0.8515 (mt) cc_final: 0.7650 (mp) REVERT: C 82 MET cc_start: 0.6921 (pmm) cc_final: 0.6495 (ptm) REVERT: C 158 PHE cc_start: 0.8223 (m-80) cc_final: 0.7923 (m-10) REVERT: C 187 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7917 (ttt) REVERT: D 82 MET cc_start: 0.7109 (mmm) cc_final: 0.6565 (ptt) REVERT: D 85 GLN cc_start: 0.8670 (mt0) cc_final: 0.8102 (mp10) REVERT: D 106 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8924 (mp) REVERT: E 59 GLU cc_start: 0.8175 (tp30) cc_final: 0.7957 (tm-30) outliers start: 45 outliers final: 35 residues processed: 177 average time/residue: 0.2318 time to fit residues: 58.1673 Evaluate side-chains 172 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 179 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 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 187 MET 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 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 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 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 147 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 4 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 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 = 0.3334 r_free = 0.3334 target = 0.104352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.085790 restraints weight = 18292.627| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.38 r_work: 0.2937 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 10850 Z= 0.393 Angle : 0.679 7.482 14675 Z= 0.333 Chirality : 0.049 0.203 1610 Planarity : 0.004 0.042 1850 Dihedral : 11.116 117.037 1516 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 5.68 % Allowed : 10.83 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.42 (0.22), residues: 1325 helix: -2.07 (0.29), residues: 265 sheet: -1.22 (0.25), residues: 385 loop : -1.56 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 81 PHE 0.017 0.002 PHE D 158 TYR 0.021 0.002 TYR B 56 ARG 0.007 0.001 ARG A 130 *********************** 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 193 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 128 time to evaluate : 1.189 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: 0.4847 (OUTLIER) cc_final: 0.2846 (mt-10) REVERT: A 144 HIS cc_start: 0.7198 (OUTLIER) cc_final: 0.6334 (p90) REVERT: A 190 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.6302 (m-70) REVERT: B 82 MET cc_start: 0.7041 (mmm) cc_final: 0.6287 (ptp) REVERT: B 233 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8350 (mm-30) REVERT: B 248 LEU cc_start: 0.8579 (mt) cc_final: 0.7673 (mp) REVERT: C 158 PHE cc_start: 0.8359 (m-80) cc_final: 0.7985 (m-10) REVERT: C 187 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7995 (ttt) REVERT: D 82 MET cc_start: 0.7291 (mmm) cc_final: 0.6885 (pmm) REVERT: D 85 GLN cc_start: 0.8730 (mt0) cc_final: 0.8081 (mp10) REVERT: D 148 MET cc_start: 0.7352 (ttt) cc_final: 0.6977 (mtp) outliers start: 65 outliers final: 48 residues processed: 177 average time/residue: 0.2201 time to fit residues: 55.8571 Evaluate side-chains 172 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 120 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 212 CYS Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 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 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 216 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 243 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 46 GLU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 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: 0.9990 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 0.0980 chunk 103 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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** D 124 GLN E 85 GLN E 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.090580 restraints weight = 18289.724| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.40 r_work: 0.3021 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10850 Z= 0.168 Angle : 0.579 10.563 14675 Z= 0.278 Chirality : 0.045 0.144 1610 Planarity : 0.003 0.036 1850 Dihedral : 10.157 102.803 1516 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.10 % Allowed : 12.40 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.14 (0.22), residues: 1325 helix: -1.74 (0.30), residues: 265 sheet: -0.99 (0.26), residues: 385 loop : -1.47 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 81 PHE 0.009 0.001 PHE E 141 TYR 0.018 0.001 TYR E 256 ARG 0.006 0.001 ARG A 130 *********************** 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 194 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.3774 (OUTLIER) cc_final: 0.1547 (mt-10) REVERT: A 82 MET cc_start: 0.6647 (mmp) cc_final: 0.4923 (ptp) REVERT: A 87 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8399 (mtm-85) REVERT: A 190 HIS cc_start: 0.6893 (OUTLIER) cc_final: 0.5550 (m-70) REVERT: B 82 MET cc_start: 0.7117 (mmm) cc_final: 0.6389 (ptp) REVERT: B 233 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8288 (mm-30) REVERT: B 248 LEU cc_start: 0.8518 (mt) cc_final: 0.7565 (mp) REVERT: C 158 PHE cc_start: 0.8306 (m-80) cc_final: 0.8033 (m-10) REVERT: C 187 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7933 (ttt) REVERT: D 82 MET cc_start: 0.7387 (mmm) cc_final: 0.6880 (ptt) REVERT: D 85 GLN cc_start: 0.8697 (mt0) cc_final: 0.8156 (mp10) REVERT: D 148 MET cc_start: 0.7213 (ttt) cc_final: 0.6896 (mtp) REVERT: D 151 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7536 (mt-10) REVERT: E 47 ARG cc_start: 0.8769 (ttt180) cc_final: 0.8433 (ttt-90) REVERT: E 124 GLN cc_start: 0.7182 (pt0) cc_final: 0.6828 (pt0) REVERT: E 130 ARG cc_start: 0.8105 (ttm110) cc_final: 0.7866 (ttm110) outliers start: 47 outliers final: 34 residues processed: 177 average time/residue: 0.2386 time to fit residues: 59.3847 Evaluate side-chains 166 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 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 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 81 HIS 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 259 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain 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 190 HIS Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 243 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 9 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 E 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.108187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.089891 restraints weight = 18557.459| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.40 r_work: 0.3005 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5022 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= 0.202 Angle : 0.589 8.852 14675 Z= 0.283 Chirality : 0.045 0.139 1610 Planarity : 0.003 0.033 1850 Dihedral : 10.018 103.478 1516 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.19 % Allowed : 12.66 % Favored : 83.14 % 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: -2.17 (0.22), residues: 1325 helix: -1.99 (0.27), residues: 305 sheet: -0.67 (0.24), residues: 425 loop : -1.59 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 81 PHE 0.009 0.001 PHE D 158 TYR 0.020 0.001 TYR E 256 ARG 0.005 0.001 ARG A 130 *********************** 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 186 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4036 (OUTLIER) cc_final: 0.2115 (mt-10) REVERT: A 82 MET cc_start: 0.6867 (mmp) cc_final: 0.5061 (ptp) REVERT: A 87 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8396 (mtm-85) REVERT: A 190 HIS cc_start: 0.6951 (OUTLIER) cc_final: 0.5584 (m-70) REVERT: B 82 MET cc_start: 0.7361 (mmm) cc_final: 0.6386 (ptp) REVERT: B 87 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7714 (mtm-85) REVERT: B 233 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8301 (mm-30) REVERT: B 248 LEU cc_start: 0.8528 (mt) cc_final: 0.7595 (mp) REVERT: B 251 ASP cc_start: 0.7598 (t70) cc_final: 0.7279 (t70) REVERT: C 158 PHE cc_start: 0.8339 (m-80) cc_final: 0.7972 (m-10) REVERT: C 187 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8010 (ttt) REVERT: C 202 MET cc_start: 0.8364 (tpp) cc_final: 0.8019 (tpp) REVERT: D 82 MET cc_start: 0.7520 (mmm) cc_final: 0.6962 (ptt) REVERT: D 85 GLN cc_start: 0.8703 (mt0) cc_final: 0.8162 (mp10) REVERT: D 148 MET cc_start: 0.7385 (ttt) cc_final: 0.6951 (mtp) REVERT: E 47 ARG cc_start: 0.8790 (ttt180) cc_final: 0.8511 (ttt-90) REVERT: E 124 GLN cc_start: 0.7286 (pt0) cc_final: 0.6933 (pt0) REVERT: E 130 ARG cc_start: 0.8118 (ttm110) cc_final: 0.7788 (ttm170) outliers start: 48 outliers final: 37 residues processed: 169 average time/residue: 0.2434 time to fit residues: 57.9471 Evaluate side-chains 172 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 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 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 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 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 259 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 72 MET 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 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 177 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 243 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 54 optimal weight: 0.4980 chunk 122 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN E 81 HIS E 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.090727 restraints weight = 18212.650| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.44 r_work: 0.3014 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10850 Z= 0.172 Angle : 0.572 7.925 14675 Z= 0.276 Chirality : 0.045 0.138 1610 Planarity : 0.003 0.035 1850 Dihedral : 9.772 100.169 1516 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.19 % Allowed : 12.40 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.22), residues: 1325 helix: -1.82 (0.27), residues: 305 sheet: -0.54 (0.25), residues: 425 loop : -1.55 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 81 PHE 0.008 0.001 PHE D 139 TYR 0.023 0.001 TYR E 256 ARG 0.008 0.001 ARG D 130 *********************** 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 183 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.3675 (OUTLIER) cc_final: 0.1754 (mt-10) REVERT: A 82 MET cc_start: 0.7044 (mmp) cc_final: 0.5120 (ptp) REVERT: A 190 HIS cc_start: 0.6701 (OUTLIER) cc_final: 0.5382 (m-70) REVERT: B 82 MET cc_start: 0.7457 (mmm) cc_final: 0.6455 (ptp) REVERT: B 233 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8289 (mm-30) REVERT: B 248 LEU cc_start: 0.8519 (mt) cc_final: 0.7560 (mp) REVERT: C 158 PHE cc_start: 0.8353 (m-80) cc_final: 0.8041 (m-10) REVERT: C 187 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8007 (ttt) REVERT: C 202 MET cc_start: 0.8348 (tpp) cc_final: 0.8104 (tpp) REVERT: D 82 MET cc_start: 0.7527 (mmm) cc_final: 0.6948 (ptt) REVERT: D 85 GLN cc_start: 0.8726 (mt0) cc_final: 0.8213 (mp10) REVERT: D 148 MET cc_start: 0.7426 (ttt) cc_final: 0.6973 (mtp) REVERT: E 47 ARG cc_start: 0.8776 (ttt180) cc_final: 0.8459 (ttt-90) REVERT: E 124 GLN cc_start: 0.7356 (pt0) cc_final: 0.7038 (pt0) REVERT: E 130 ARG cc_start: 0.8114 (ttm110) cc_final: 0.7738 (ttm170) outliers start: 48 outliers final: 37 residues processed: 165 average time/residue: 0.2313 time to fit residues: 54.3188 Evaluate side-chains 169 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 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 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 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 72 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 HIS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 37 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS B 81 HIS B 85 GLN 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 = 0.3351 r_free = 0.3351 target = 0.105481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.087165 restraints weight = 18618.576| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.35 r_work: 0.2937 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10850 Z= 0.331 Angle : 0.649 7.519 14675 Z= 0.315 Chirality : 0.047 0.149 1610 Planarity : 0.004 0.056 1850 Dihedral : 10.213 103.273 1516 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 4.54 % Allowed : 12.31 % Favored : 83.14 % 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: -1.91 (0.22), residues: 1325 helix: -1.61 (0.30), residues: 260 sheet: -0.81 (0.26), residues: 385 loop : -1.32 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 81 PHE 0.013 0.002 PHE D 158 TYR 0.026 0.002 TYR D 256 ARG 0.008 0.001 ARG A 130 *********************** 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 174 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.4733 (OUTLIER) cc_final: 0.2563 (mt-10) REVERT: A 82 MET cc_start: 0.7007 (mmp) cc_final: 0.5127 (ptp) REVERT: A 190 HIS cc_start: 0.7413 (OUTLIER) cc_final: 0.5955 (m-70) REVERT: B 82 MET cc_start: 0.7541 (mmm) cc_final: 0.6414 (ptt) REVERT: B 87 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7826 (mtm-85) REVERT: B 233 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8343 (mm-30) REVERT: B 248 LEU cc_start: 0.8597 (mt) cc_final: 0.7665 (mp) REVERT: C 158 PHE cc_start: 0.8431 (m-80) cc_final: 0.8035 (m-10) REVERT: C 187 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7998 (ttt) REVERT: D 82 MET cc_start: 0.7595 (mmm) cc_final: 0.7040 (ptt) REVERT: D 85 GLN cc_start: 0.8743 (mt0) cc_final: 0.8202 (mp10) REVERT: D 148 MET cc_start: 0.7464 (ttt) cc_final: 0.7042 (mtp) REVERT: D 256 TYR cc_start: 0.8766 (m-80) cc_final: 0.8446 (m-80) REVERT: E 124 GLN cc_start: 0.7279 (pt0) cc_final: 0.6976 (pt0) outliers start: 52 outliers final: 39 residues processed: 161 average time/residue: 0.2296 time to fit residues: 52.6257 Evaluate side-chains 162 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 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 C residue 5 THR Chi-restraints excluded: chain C residue 54 ASP 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 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 72 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 HIS 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 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: 0.9980 chunk 4 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.0170 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 199 ASN E 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.090646 restraints weight = 18332.098| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.46 r_work: 0.2996 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10850 Z= 0.165 Angle : 0.582 7.273 14675 Z= 0.281 Chirality : 0.045 0.138 1610 Planarity : 0.003 0.034 1850 Dihedral : 9.676 100.391 1516 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.93 % Allowed : 12.84 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.85 (0.23), residues: 1325 helix: -1.59 (0.28), residues: 300 sheet: -0.47 (0.25), residues: 425 loop : -1.49 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 81 PHE 0.008 0.001 PHE E 141 TYR 0.021 0.001 TYR E 56 ARG 0.010 0.001 ARG D 130 ********************** 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 185 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.3724 (OUTLIER) cc_final: 0.1762 (mt-10) REVERT: A 82 MET cc_start: 0.7236 (mmp) cc_final: 0.5337 (ptp) REVERT: A 190 HIS cc_start: 0.6764 (OUTLIER) cc_final: 0.5458 (m-70) REVERT: B 82 MET cc_start: 0.7643 (mmm) cc_final: 0.6485 (ptt) REVERT: B 83 GLU cc_start: 0.8501 (mp0) cc_final: 0.7988 (mp0) REVERT: B 87 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7710 (mtm-85) REVERT: B 233 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8243 (mm-30) REVERT: B 248 LEU cc_start: 0.8538 (mt) cc_final: 0.7605 (mp) REVERT: D 82 MET cc_start: 0.7559 (mmm) cc_final: 0.6977 (ptt) REVERT: D 85 GLN cc_start: 0.8733 (mt0) cc_final: 0.8234 (mp10) REVERT: D 148 MET cc_start: 0.7447 (ttt) cc_final: 0.7002 (mtp) REVERT: D 256 TYR cc_start: 0.8648 (m-80) cc_final: 0.8188 (m-10) REVERT: E 47 ARG cc_start: 0.8751 (ttt180) cc_final: 0.8398 (ttt-90) REVERT: E 124 GLN cc_start: 0.7317 (pt0) cc_final: 0.7008 (pt0) outliers start: 45 outliers final: 36 residues processed: 168 average time/residue: 0.2277 time to fit residues: 54.7611 Evaluate side-chains 166 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 212 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 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 C residue 5 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 HIS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 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 57 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 81 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.108083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.090079 restraints weight = 18306.274| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.33 r_work: 0.3011 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.003 0.029 10850 Z= 0.209 Angle : 0.595 7.013 14675 Z= 0.287 Chirality : 0.045 0.138 1610 Planarity : 0.003 0.035 1850 Dihedral : 9.672 100.689 1516 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.67 % Allowed : 13.36 % 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: -1.77 (0.23), residues: 1325 helix: -1.51 (0.28), residues: 290 sheet: -0.44 (0.25), residues: 425 loop : -1.44 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 81 PHE 0.008 0.001 PHE D 158 TYR 0.022 0.001 TYR D 256 ARG 0.008 0.001 ARG A 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4100.88 seconds wall clock time: 74 minutes 20.43 seconds (4460.43 seconds total)