Starting phenix.real_space_refine on Tue Jul 29 10:33:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e26_30952/07_2025/7e26_30952.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e26_30952/07_2025/7e26_30952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e26_30952/07_2025/7e26_30952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e26_30952/07_2025/7e26_30952.map" model { file = "/net/cci-nas-00/data/ceres_data/7e26_30952/07_2025/7e26_30952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e26_30952/07_2025/7e26_30952.cif" } resolution = 2.29 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= 0.006 sd= 0.066 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 7515 2.51 5 N 1765 2.21 5 O 2010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11360 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 7.73, per 1000 atoms: 0.68 Number of scatterers: 11360 At special positions: 0 Unit cell: (96.4678, 96.4678, 82.9758, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2010 8.00 N 1765 7.00 C 7515 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: 2.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2650 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 1 sheets defined 81.0% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'D' and resid 20 through 35 removed outlier: 3.509A pdb=" N LYS D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 68 removed outlier: 3.865A pdb=" N PHE D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 91 through 101 removed outlier: 4.071A pdb=" N MET D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR D 100 " --> pdb=" O CYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 4.444A pdb=" N LEU D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 148 Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.551A pdb=" N PHE D 169 " --> pdb=" O HIS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 206 removed outlier: 3.764A pdb=" N PHE D 195 " --> pdb=" O GLY D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 227 removed outlier: 3.976A pdb=" N SER D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 216 " --> pdb=" O TYR D 212 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.575A pdb=" N ASN D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 257 through 271 removed outlier: 3.514A pdb=" N GLY D 269 " --> pdb=" O ASN D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 291 removed outlier: 3.515A pdb=" N LEU D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS D 284 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.509A pdb=" N LYS A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 68 removed outlier: 3.864A pdb=" N PHE A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.071A pdb=" N MET A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 118 removed outlier: 4.444A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 148 Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.551A pdb=" N PHE A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 206 removed outlier: 3.764A pdb=" N PHE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 227 removed outlier: 3.976A pdb=" N SER A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.575A pdb=" N ASN A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 257 through 271 removed outlier: 3.515A pdb=" N GLY A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 291 removed outlier: 3.516A pdb=" N LEU A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLU A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 35 removed outlier: 3.509A pdb=" N LYS B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 35 " --> pdb=" O TYR B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 68 removed outlier: 3.866A pdb=" N PHE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.520A pdb=" N THR B 100 " --> pdb=" O CYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 removed outlier: 4.444A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 148 Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.551A pdb=" N PHE B 169 " --> pdb=" O HIS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 206 removed outlier: 3.764A pdb=" N PHE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 226 removed outlier: 3.976A pdb=" N SER B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.574A pdb=" N ASN B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 257 through 271 removed outlier: 3.514A pdb=" N GLY B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 291 removed outlier: 3.516A pdb=" N LEU B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N HIS B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 35 removed outlier: 3.510A pdb=" N LYS C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 68 removed outlier: 3.865A pdb=" N PHE C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 101 removed outlier: 4.071A pdb=" N MET C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 100 " --> pdb=" O CYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 118 removed outlier: 4.443A pdb=" N LEU C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 148 Processing helix chain 'C' and resid 164 through 177 removed outlier: 3.551A pdb=" N PHE C 169 " --> pdb=" O HIS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 206 removed outlier: 3.763A pdb=" N PHE C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 227 removed outlier: 3.977A pdb=" N SER C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.575A pdb=" N ASN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 257 through 271 removed outlier: 3.514A pdb=" N GLY C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 291 removed outlier: 3.516A pdb=" N LEU C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 35 removed outlier: 3.509A pdb=" N LYS E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS E 35 " --> pdb=" O TYR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 68 removed outlier: 3.865A pdb=" N PHE E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 Processing helix chain 'E' and resid 79 through 90 Processing helix chain 'E' and resid 91 through 101 removed outlier: 4.070A pdb=" N MET E 95 " --> pdb=" O PRO E 91 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR E 100 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.444A pdb=" N LEU E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 148 Processing helix chain 'E' and resid 164 through 177 removed outlier: 3.551A pdb=" N PHE E 169 " --> pdb=" O HIS E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 206 removed outlier: 3.764A pdb=" N PHE E 195 " --> pdb=" O GLY E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 227 removed outlier: 3.977A pdb=" N SER E 215 " --> pdb=" O GLY E 211 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY E 227 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.575A pdb=" N ASN E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 255 Processing helix chain 'E' and resid 257 through 271 removed outlier: 3.514A pdb=" N GLY E 269 " --> pdb=" O ASN E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 291 removed outlier: 3.516A pdb=" N LEU E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU E 283 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16 removed outlier: 7.314A pdb=" N SER B 14 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE C 15 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS B 16 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N SER A 14 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE B 15 " --> pdb=" O SER A 14 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LYS A 16 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL A 13 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N SER D 14 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE E 15 " --> pdb=" O SER D 14 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS D 16 " --> pdb=" O ILE E 15 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.25: 1675 1.25 - 1.39: 3321 1.39 - 1.53: 5983 1.53 - 1.67: 496 1.67 - 1.81: 100 Bond restraints: 11575 Sorted by residual: bond pdb=" C HIS A 230 " pdb=" O HIS A 230 " ideal model delta sigma weight residual 1.235 1.116 0.118 1.18e-02 7.18e+03 1.01e+02 bond pdb=" C HIS B 284 " pdb=" O HIS B 284 " ideal model delta sigma weight residual 1.237 1.126 0.110 1.19e-02 7.06e+03 8.57e+01 bond pdb=" C LEU A 259 " pdb=" O LEU A 259 " ideal model delta sigma weight residual 1.244 1.159 0.084 9.40e-03 1.13e+04 8.02e+01 bond pdb=" C ASN B 287 " pdb=" O ASN B 287 " ideal model delta sigma weight residual 1.237 1.150 0.086 1.16e-02 7.43e+03 5.55e+01 bond pdb=" CA HIS B 284 " pdb=" C HIS B 284 " ideal model delta sigma weight residual 1.524 1.428 0.095 1.29e-02 6.01e+03 5.47e+01 ... (remaining 11570 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 14823 1.81 - 3.62: 715 3.62 - 5.43: 100 5.43 - 7.23: 33 7.23 - 9.04: 19 Bond angle restraints: 15690 Sorted by residual: angle pdb=" N ARG D 290 " pdb=" CA ARG D 290 " pdb=" C ARG D 290 " ideal model delta sigma weight residual 112.23 103.87 8.36 1.26e+00 6.30e-01 4.40e+01 angle pdb=" N THR B 181 " pdb=" CA THR B 181 " pdb=" C THR B 181 " ideal model delta sigma weight residual 110.36 102.22 8.14 1.55e+00 4.16e-01 2.76e+01 angle pdb=" N HIS A 179 " pdb=" CA HIS A 179 " pdb=" C HIS A 179 " ideal model delta sigma weight residual 112.92 119.19 -6.27 1.23e+00 6.61e-01 2.60e+01 angle pdb=" N THR A 181 " pdb=" CA THR A 181 " pdb=" C THR A 181 " ideal model delta sigma weight residual 110.59 103.55 7.04 1.45e+00 4.76e-01 2.36e+01 angle pdb=" CA HIS A 230 " pdb=" C HIS A 230 " pdb=" N ILE A 231 " ideal model delta sigma weight residual 115.96 122.22 -6.26 1.29e+00 6.01e-01 2.35e+01 ... (remaining 15685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 5840 15.85 - 31.70: 600 31.70 - 47.55: 92 47.55 - 63.40: 48 63.40 - 79.25: 10 Dihedral angle restraints: 6590 sinusoidal: 2395 harmonic: 4195 Sorted by residual: dihedral pdb=" C HIS A 179 " pdb=" N HIS A 179 " pdb=" CA HIS A 179 " pdb=" CB HIS A 179 " ideal model delta harmonic sigma weight residual -122.60 -132.17 9.57 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" C HIS C 179 " pdb=" N HIS C 179 " pdb=" CA HIS C 179 " pdb=" CB HIS C 179 " ideal model delta harmonic sigma weight residual -122.60 -131.85 9.25 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" N HIS A 179 " pdb=" C HIS A 179 " pdb=" CA HIS A 179 " pdb=" CB HIS A 179 " ideal model delta harmonic sigma weight residual 122.80 131.74 -8.94 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 6587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1619 0.093 - 0.187: 140 0.187 - 0.280: 20 0.280 - 0.373: 2 0.373 - 0.466: 9 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CA HIS A 179 " pdb=" N HIS A 179 " pdb=" C HIS A 179 " pdb=" CB HIS A 179 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA PHE C 94 " pdb=" N PHE C 94 " pdb=" C PHE C 94 " pdb=" CB PHE C 94 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA PHE E 94 " pdb=" N PHE E 94 " pdb=" C PHE E 94 " pdb=" CB PHE E 94 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.20e+00 ... (remaining 1787 not shown) Planarity restraints: 1915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 94 " 0.032 2.00e-02 2.50e+03 2.20e-02 8.45e+00 pdb=" CG PHE D 94 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE D 94 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 94 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 94 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE D 94 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 94 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 284 " -0.027 2.00e-02 2.50e+03 2.35e-02 8.31e+00 pdb=" CG HIS B 284 " 0.049 2.00e-02 2.50e+03 pdb=" ND1 HIS B 284 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS B 284 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS B 284 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS B 284 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 94 " -0.030 2.00e-02 2.50e+03 2.15e-02 8.07e+00 pdb=" CG PHE E 94 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE E 94 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE E 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 94 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE E 94 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE E 94 " -0.008 2.00e-02 2.50e+03 ... (remaining 1912 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3636 2.83 - 3.35: 10417 3.35 - 3.86: 20716 3.86 - 4.38: 25001 4.38 - 4.90: 42248 Nonbonded interactions: 102018 Sorted by model distance: nonbonded pdb=" OH TYR A 25 " pdb=" OE2 GLU A 118 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR D 25 " pdb=" OE2 GLU D 118 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR B 25 " pdb=" OE2 GLU B 118 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR E 25 " pdb=" OE2 GLU E 118 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR C 25 " pdb=" OE2 GLU C 118 " model vdw 2.314 3.040 ... (remaining 102013 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: 0.09 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: 3.060 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.340 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.009 0.118 11575 Z= 0.520 Angle : 0.931 9.042 15690 Z= 0.565 Chirality : 0.064 0.466 1790 Planarity : 0.006 0.033 1915 Dihedral : 14.053 79.249 3940 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.19 % Allowed : 2.37 % Favored : 96.44 % 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: -2.93 (0.17), residues: 1425 helix: -1.59 (0.12), residues: 1140 sheet: None (None), residues: 0 loop : -2.56 (0.30), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.002 HIS B 284 PHE 0.047 0.004 PHE E 94 TYR 0.044 0.003 TYR C 212 ARG 0.006 0.001 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.12130 ( 793) hydrogen bonds : angle 5.84586 ( 2376) covalent geometry : bond 0.00881 (11575) covalent geometry : angle 0.93135 (15690) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.246 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 140 average time/residue: 1.4304 time to fit residues: 215.8009 Evaluate side-chains 101 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 178 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.099321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.086871 restraints weight = 13982.821| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.71 r_work: 0.2925 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 11575 Z= 0.123 Angle : 0.499 7.611 15690 Z= 0.278 Chirality : 0.039 0.152 1790 Planarity : 0.003 0.023 1915 Dihedral : 5.653 50.573 1587 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.63 % Allowed : 5.68 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1425 helix: 0.31 (0.15), residues: 1145 sheet: None (None), residues: 0 loop : -1.84 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 284 PHE 0.020 0.002 PHE E 223 TYR 0.013 0.001 TYR B 212 ARG 0.001 0.000 ARG D 293 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 793) hydrogen bonds : angle 4.05778 ( 2376) covalent geometry : bond 0.00266 (11575) covalent geometry : angle 0.49878 (15690) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 1.309 Fit side-chains REVERT: B 124 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7461 (mp) REVERT: C 114 MET cc_start: 0.7366 (mtt) cc_final: 0.6933 (mmt) REVERT: C 283 GLU cc_start: 0.6769 (pm20) cc_final: 0.6440 (tp30) REVERT: E 283 GLU cc_start: 0.6762 (pm20) cc_final: 0.6359 (tp30) outliers start: 31 outliers final: 3 residues processed: 119 average time/residue: 1.2686 time to fit residues: 163.5857 Evaluate side-chains 93 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 15 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 97 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.099271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.086698 restraints weight = 14123.109| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.74 r_work: 0.2918 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11575 Z= 0.113 Angle : 0.477 7.698 15690 Z= 0.264 Chirality : 0.038 0.150 1790 Planarity : 0.003 0.022 1915 Dihedral : 4.472 42.511 1572 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.69 % Allowed : 8.31 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1425 helix: 1.11 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.92 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 59 PHE 0.015 0.001 PHE E 223 TYR 0.011 0.001 TYR E 236 ARG 0.000 0.000 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 793) hydrogen bonds : angle 3.82143 ( 2376) covalent geometry : bond 0.00236 (11575) covalent geometry : angle 0.47732 (15690) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 1.246 Fit side-chains REVERT: A 42 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.7157 (t0) REVERT: B 42 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7199 (t0) REVERT: B 283 GLU cc_start: 0.6864 (tp30) cc_final: 0.6082 (pm20) REVERT: C 42 ASN cc_start: 0.7459 (OUTLIER) cc_final: 0.7147 (t0) REVERT: C 114 MET cc_start: 0.7369 (mtt) cc_final: 0.6982 (mmt) REVERT: C 119 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7222 (mttp) REVERT: E 42 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.7083 (t0) outliers start: 20 outliers final: 6 residues processed: 108 average time/residue: 1.2676 time to fit residues: 148.5180 Evaluate side-chains 105 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.099053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.086444 restraints weight = 14083.531| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.75 r_work: 0.2914 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11575 Z= 0.114 Angle : 0.474 7.733 15690 Z= 0.261 Chirality : 0.038 0.149 1790 Planarity : 0.002 0.019 1915 Dihedral : 4.254 18.541 1570 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.12 % Allowed : 10.00 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.14 (0.22), residues: 1425 helix: 1.42 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.87 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 59 PHE 0.014 0.001 PHE D 223 TYR 0.010 0.001 TYR C 251 ARG 0.000 0.000 ARG E 290 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 793) hydrogen bonds : angle 3.75542 ( 2376) covalent geometry : bond 0.00242 (11575) covalent geometry : angle 0.47381 (15690) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 1.245 Fit side-chains REVERT: D 283 GLU cc_start: 0.6930 (pm20) cc_final: 0.6471 (tp30) REVERT: A 42 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.7230 (t0) REVERT: A 283 GLU cc_start: 0.6801 (pm20) cc_final: 0.6355 (tp30) REVERT: B 42 ASN cc_start: 0.7566 (OUTLIER) cc_final: 0.7271 (t0) REVERT: B 124 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7598 (mp) REVERT: B 283 GLU cc_start: 0.6968 (tp30) cc_final: 0.6159 (pm20) REVERT: C 42 ASN cc_start: 0.7511 (OUTLIER) cc_final: 0.7169 (t0) REVERT: C 114 MET cc_start: 0.7462 (mtt) cc_final: 0.7055 (mmt) REVERT: C 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7160 (mttt) REVERT: E 42 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.7144 (t0) REVERT: E 283 GLU cc_start: 0.6818 (pm20) cc_final: 0.6368 (tp30) outliers start: 25 outliers final: 7 residues processed: 115 average time/residue: 1.2211 time to fit residues: 153.1292 Evaluate side-chains 108 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 35 optimal weight: 0.0050 chunk 66 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.100327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.087811 restraints weight = 13833.705| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.73 r_work: 0.2935 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11575 Z= 0.104 Angle : 0.457 7.643 15690 Z= 0.251 Chirality : 0.037 0.144 1790 Planarity : 0.002 0.019 1915 Dihedral : 4.142 18.151 1570 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.46 % Allowed : 9.83 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.42 (0.22), residues: 1425 helix: 1.63 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.83 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 59 PHE 0.013 0.001 PHE D 223 TYR 0.011 0.001 TYR C 251 ARG 0.000 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 793) hydrogen bonds : angle 3.68338 ( 2376) covalent geometry : bond 0.00215 (11575) covalent geometry : angle 0.45656 (15690) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 1.292 Fit side-chains REVERT: D 283 GLU cc_start: 0.6871 (pm20) cc_final: 0.6421 (tp30) REVERT: A 42 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.7200 (t0) REVERT: B 124 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7569 (mp) REVERT: B 201 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.7459 (t80) REVERT: B 283 GLU cc_start: 0.6969 (tp30) cc_final: 0.6269 (pm20) REVERT: C 42 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.7135 (t0) REVERT: C 114 MET cc_start: 0.7464 (mtt) cc_final: 0.7018 (mmt) REVERT: C 119 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7092 (mttt) REVERT: E 42 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.7127 (t0) outliers start: 29 outliers final: 8 residues processed: 124 average time/residue: 1.1697 time to fit residues: 158.3604 Evaluate side-chains 111 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.097892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.085356 restraints weight = 14115.136| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.74 r_work: 0.2903 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11575 Z= 0.123 Angle : 0.485 7.785 15690 Z= 0.266 Chirality : 0.038 0.152 1790 Planarity : 0.002 0.020 1915 Dihedral : 4.221 18.428 1570 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.95 % Allowed : 11.19 % Favored : 86.86 % 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: 1.44 (0.22), residues: 1425 helix: 1.63 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.78 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 59 PHE 0.014 0.001 PHE D 223 TYR 0.011 0.001 TYR B 31 ARG 0.001 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 793) hydrogen bonds : angle 3.73297 ( 2376) covalent geometry : bond 0.00271 (11575) covalent geometry : angle 0.48485 (15690) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.173 Fit side-chains REVERT: D 119 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7264 (mttt) REVERT: D 283 GLU cc_start: 0.6813 (pm20) cc_final: 0.6419 (tp30) REVERT: A 42 ASN cc_start: 0.7495 (OUTLIER) cc_final: 0.7147 (t0) REVERT: B 124 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7457 (mp) REVERT: B 283 GLU cc_start: 0.6892 (tp30) cc_final: 0.6160 (pm20) REVERT: C 42 ASN cc_start: 0.7463 (OUTLIER) cc_final: 0.7121 (t0) REVERT: C 114 MET cc_start: 0.7390 (mtt) cc_final: 0.6962 (mmt) REVERT: E 42 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.7018 (t0) REVERT: E 283 GLU cc_start: 0.6741 (pm20) cc_final: 0.6299 (tp30) outliers start: 23 outliers final: 11 residues processed: 114 average time/residue: 1.3007 time to fit residues: 160.9373 Evaluate side-chains 113 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 41 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN D 59 HIS ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.092627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.080082 restraints weight = 14379.347| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.74 r_work: 0.2820 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 11575 Z= 0.269 Angle : 0.622 8.218 15690 Z= 0.340 Chirality : 0.047 0.175 1790 Planarity : 0.003 0.021 1915 Dihedral : 4.680 18.528 1570 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.29 % Allowed : 10.93 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1425 helix: 1.15 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.68 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS B 59 PHE 0.022 0.003 PHE D 223 TYR 0.013 0.002 TYR E 221 ARG 0.001 0.000 ARG C 293 Details of bonding type rmsd hydrogen bonds : bond 0.06070 ( 793) hydrogen bonds : angle 4.09304 ( 2376) covalent geometry : bond 0.00664 (11575) covalent geometry : angle 0.62216 (15690) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 1.175 Fit side-chains REVERT: D 119 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7359 (mttp) REVERT: A 42 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.7539 (t0) REVERT: B 124 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7552 (mp) REVERT: B 283 GLU cc_start: 0.6970 (tp30) cc_final: 0.6006 (pm20) REVERT: C 42 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7580 (t0) REVERT: C 114 MET cc_start: 0.7527 (mtt) cc_final: 0.7177 (mmt) REVERT: C 119 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7188 (mttt) REVERT: E 42 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7345 (t0) outliers start: 27 outliers final: 14 residues processed: 118 average time/residue: 1.2677 time to fit residues: 162.0275 Evaluate side-chains 118 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.094672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.082123 restraints weight = 14227.818| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.74 r_work: 0.2853 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11575 Z= 0.162 Angle : 0.536 8.337 15690 Z= 0.294 Chirality : 0.041 0.160 1790 Planarity : 0.003 0.022 1915 Dihedral : 4.527 18.536 1570 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.20 % Allowed : 11.44 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.22), residues: 1425 helix: 1.34 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.64 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 165 PHE 0.017 0.002 PHE D 223 TYR 0.011 0.002 TYR C 31 ARG 0.001 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 793) hydrogen bonds : angle 3.93919 ( 2376) covalent geometry : bond 0.00378 (11575) covalent geometry : angle 0.53594 (15690) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.194 Fit side-chains REVERT: D 119 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7284 (mttt) REVERT: D 283 GLU cc_start: 0.6816 (pm20) cc_final: 0.6370 (tp30) REVERT: A 42 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.7273 (t0) REVERT: B 124 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7439 (mp) REVERT: B 283 GLU cc_start: 0.6940 (tp30) cc_final: 0.6220 (pm20) REVERT: C 42 ASN cc_start: 0.7576 (OUTLIER) cc_final: 0.7281 (t0) REVERT: C 114 MET cc_start: 0.7392 (mtt) cc_final: 0.6957 (mmt) REVERT: C 119 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7094 (mttt) REVERT: E 42 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7123 (t0) outliers start: 26 outliers final: 12 residues processed: 117 average time/residue: 1.5504 time to fit residues: 196.5452 Evaluate side-chains 117 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.098039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.085371 restraints weight = 14195.836| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.75 r_work: 0.2896 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11575 Z= 0.117 Angle : 0.487 9.519 15690 Z= 0.266 Chirality : 0.038 0.150 1790 Planarity : 0.003 0.021 1915 Dihedral : 4.287 18.262 1570 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.86 % Allowed : 11.78 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.22), residues: 1425 helix: 1.64 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.72 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 165 PHE 0.014 0.001 PHE D 223 TYR 0.010 0.001 TYR C 31 ARG 0.001 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 793) hydrogen bonds : angle 3.76691 ( 2376) covalent geometry : bond 0.00253 (11575) covalent geometry : angle 0.48656 (15690) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.182 Fit side-chains REVERT: D 56 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6976 (tp) REVERT: D 119 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7330 (mttt) REVERT: D 283 GLU cc_start: 0.6868 (pm20) cc_final: 0.6411 (tp30) REVERT: A 42 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7161 (t0) REVERT: B 124 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7516 (mp) REVERT: B 283 GLU cc_start: 0.7008 (tp30) cc_final: 0.6279 (pm20) REVERT: C 42 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7173 (t0) REVERT: C 114 MET cc_start: 0.7428 (mtt) cc_final: 0.7013 (mmt) REVERT: C 119 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7131 (mttt) REVERT: E 42 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7146 (t0) REVERT: E 283 GLU cc_start: 0.6877 (pm20) cc_final: 0.6437 (tp30) outliers start: 22 outliers final: 10 residues processed: 116 average time/residue: 1.2696 time to fit residues: 159.7476 Evaluate side-chains 116 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 92 optimal weight: 0.0980 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.098592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.085959 restraints weight = 14061.681| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.75 r_work: 0.2905 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11575 Z= 0.115 Angle : 0.486 9.729 15690 Z= 0.263 Chirality : 0.038 0.149 1790 Planarity : 0.003 0.021 1915 Dihedral : 4.213 18.263 1570 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.95 % Allowed : 12.03 % Favored : 86.02 % 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: 1.62 (0.22), residues: 1425 helix: 1.75 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.66 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 165 PHE 0.013 0.001 PHE A 223 TYR 0.011 0.001 TYR B 31 ARG 0.002 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 793) hydrogen bonds : angle 3.71632 ( 2376) covalent geometry : bond 0.00248 (11575) covalent geometry : angle 0.48561 (15690) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 1.241 Fit side-chains REVERT: D 56 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6954 (tp) REVERT: D 119 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7306 (mttt) REVERT: D 283 GLU cc_start: 0.6863 (pm20) cc_final: 0.6384 (tp30) REVERT: A 42 ASN cc_start: 0.7510 (OUTLIER) cc_final: 0.7172 (t0) REVERT: A 283 GLU cc_start: 0.6764 (pm20) cc_final: 0.6328 (tp30) REVERT: B 124 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7493 (mp) REVERT: B 283 GLU cc_start: 0.7040 (tp30) cc_final: 0.6311 (pm20) REVERT: C 42 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.7131 (t0) REVERT: C 56 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6902 (tp) REVERT: C 114 MET cc_start: 0.7459 (mtt) cc_final: 0.7035 (mmt) REVERT: C 119 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7119 (mttt) REVERT: E 42 ASN cc_start: 0.7458 (OUTLIER) cc_final: 0.7138 (t0) REVERT: E 283 GLU cc_start: 0.6851 (pm20) cc_final: 0.6374 (tp30) outliers start: 23 outliers final: 10 residues processed: 118 average time/residue: 1.2506 time to fit residues: 160.5616 Evaluate side-chains 116 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 135 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 108 optimal weight: 0.0980 chunk 20 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.099023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.086426 restraints weight = 13975.206| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.74 r_work: 0.2912 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11575 Z= 0.113 Angle : 0.482 9.502 15690 Z= 0.261 Chirality : 0.038 0.148 1790 Planarity : 0.002 0.020 1915 Dihedral : 4.179 17.930 1570 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.78 % Allowed : 12.20 % Favored : 86.02 % 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: 1.70 (0.22), residues: 1425 helix: 1.81 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.66 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 165 PHE 0.013 0.001 PHE D 223 TYR 0.011 0.001 TYR B 31 ARG 0.002 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 793) hydrogen bonds : angle 3.69582 ( 2376) covalent geometry : bond 0.00240 (11575) covalent geometry : angle 0.48158 (15690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7462.04 seconds wall clock time: 131 minutes 22.99 seconds (7882.99 seconds total)