Starting phenix.real_space_refine on Fri Jul 3 01:12:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jox_61688/07_2026/9jox_61688.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jox_61688/07_2026/9jox_61688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jox_61688/07_2026/9jox_61688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jox_61688/07_2026/9jox_61688.map" model { file = "/net/cci-nas-00/data/ceres_data/9jox_61688/07_2026/9jox_61688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jox_61688/07_2026/9jox_61688.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 S 75 5.16 5 Cl 10 4.86 5 C 7519 2.51 5 N 1595 2.21 5 O 2020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11229 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2061 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 5, 'TRANS': 257} Chain: "B" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2061 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 5, 'TRANS': 257} Chain: "C" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2061 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 5, 'TRANS': 257} Chain: "D" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2061 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 5, 'TRANS': 257} Chain: "E" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2061 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 5, 'TRANS': 257} Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 186 Ad-hoc single atom residues: {' CL': 2} Unusual residues: {'D12': 1, 'PC1': 1, 'PLC': 2, 'R16': 1, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Ad-hoc single atom residues: {' CL': 2} Unusual residues: {'8K6': 1, 'C14': 1, 'PC1': 1, 'PLC': 1, 'R16': 1, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 134 Ad-hoc single atom residues: {' CL': 2} Unusual residues: {'8K6': 1, 'PC1': 1, 'PLC': 1, 'RET': 1} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 160 Ad-hoc single atom residues: {' CL': 2} Unusual residues: {'D12': 1, 'PC1': 1, 'PLC': 1, 'R16': 2, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 120 Ad-hoc single atom residues: {' CL': 2} Unusual residues: {'C14': 1, 'PC1': 1, 'R16': 2, 'RET': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Time building chain proxies: 2.58, per 1000 atoms: 0.23 Number of scatterers: 11229 At special positions: 0 Unit cell: (93.6205, 95.2775, 82.0215, 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) Cl 10 17.00 S 75 16.00 P 10 15.00 O 2020 8.00 N 1595 7.00 C 7519 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 439.8 milliseconds 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2450 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 5 sheets defined 88.6% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 removed outlier: 3.537A pdb=" N PHE A 8 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 40 removed outlier: 3.522A pdb=" N GLY A 27 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 44 through 75 removed outlier: 4.539A pdb=" N ILE A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A 51 " --> pdb=" O TYR A 47 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 114 removed outlier: 3.698A pdb=" N TYR A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET A 100 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 3.596A pdb=" N LEU A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 144 Processing helix chain 'A' and resid 149 through 179 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 185 through 214 removed outlier: 4.379A pdb=" N THR A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Proline residue: A 205 - end of helix Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 216 through 253 removed outlier: 3.867A pdb=" N ILE A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N TYR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 263 Processing helix chain 'B' and resid 3 through 8 removed outlier: 3.531A pdb=" N PHE B 8 " --> pdb=" O GLU B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 40 removed outlier: 3.523A pdb=" N GLY B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 44 through 75 removed outlier: 4.471A pdb=" N ILE B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B 51 " --> pdb=" O TYR B 47 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 114 removed outlier: 3.753A pdb=" N TYR B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Proline residue: B 104 - end of helix removed outlier: 3.582A pdb=" N LEU B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 144 Processing helix chain 'B' and resid 149 through 179 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 185 through 214 removed outlier: 4.404A pdb=" N THR B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Proline residue: B 205 - end of helix Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 216 through 253 removed outlier: 3.866A pdb=" N ILE B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 263 Processing helix chain 'C' and resid 3 through 8 removed outlier: 3.530A pdb=" N PHE C 8 " --> pdb=" O GLU C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 40 removed outlier: 3.531A pdb=" N GLY C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 43 No H-bonds generated for 'chain 'C' and resid 41 through 43' Processing helix chain 'C' and resid 44 through 75 removed outlier: 4.497A pdb=" N ILE C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 114 removed outlier: 3.698A pdb=" N TYR C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Proline residue: C 104 - end of helix removed outlier: 3.589A pdb=" N LEU C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 144 Processing helix chain 'C' and resid 149 through 179 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 185 through 214 removed outlier: 4.379A pdb=" N THR C 189 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Proline residue: C 205 - end of helix Proline residue: C 211 - end of helix Processing helix chain 'C' and resid 216 through 253 removed outlier: 3.889A pdb=" N ILE C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 263 Processing helix chain 'D' and resid 3 through 8 removed outlier: 3.533A pdb=" N PHE D 8 " --> pdb=" O GLU D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 40 removed outlier: 3.522A pdb=" N GLY D 27 " --> pdb=" O THR D 23 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 34 " --> pdb=" O PHE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 43 No H-bonds generated for 'chain 'D' and resid 41 through 43' Processing helix chain 'D' and resid 44 through 75 removed outlier: 4.514A pdb=" N ILE D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR D 51 " --> pdb=" O TYR D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 114 removed outlier: 3.689A pdb=" N TYR D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Proline residue: D 104 - end of helix removed outlier: 3.600A pdb=" N LEU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 144 Processing helix chain 'D' and resid 149 through 179 Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 185 through 214 removed outlier: 4.370A pdb=" N THR D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) Proline residue: D 205 - end of helix Proline residue: D 211 - end of helix Processing helix chain 'D' and resid 216 through 253 removed outlier: 3.886A pdb=" N ILE D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 263 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.526A pdb=" N PHE E 8 " --> pdb=" O GLU E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 40 removed outlier: 3.536A pdb=" N GLY E 27 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE E 34 " --> pdb=" O PHE E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 44 through 75 removed outlier: 4.466A pdb=" N ILE E 49 " --> pdb=" O PRO E 45 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 114 removed outlier: 3.738A pdb=" N TYR E 96 " --> pdb=" O ASN E 92 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET E 100 " --> pdb=" O TYR E 96 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Proline residue: E 104 - end of helix removed outlier: 3.598A pdb=" N LEU E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 144 Processing helix chain 'E' and resid 149 through 179 Processing helix chain 'E' and resid 180 through 182 No H-bonds generated for 'chain 'E' and resid 180 through 182' Processing helix chain 'E' and resid 185 through 214 removed outlier: 4.405A pdb=" N THR E 189 " --> pdb=" O GLY E 185 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Proline residue: E 205 - end of helix Proline residue: E 211 - end of helix Processing helix chain 'E' and resid 216 through 253 removed outlier: 3.884A pdb=" N ILE E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TYR E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 263 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 78 Processing sheet with id=AA4, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 76 through 78 846 hydrogen bonds defined for protein. 2508 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2234 1.33 - 1.46: 3397 1.46 - 1.58: 5515 1.58 - 1.71: 21 1.71 - 1.84: 140 Bond restraints: 11307 Sorted by residual: bond pdb=" CA ALA C 77 " pdb=" CB ALA C 77 " ideal model delta sigma weight residual 1.535 1.431 0.104 2.09e-02 2.29e+03 2.48e+01 bond pdb=" CA ALA B 77 " pdb=" CB ALA B 77 " ideal model delta sigma weight residual 1.535 1.436 0.099 2.09e-02 2.29e+03 2.26e+01 bond pdb=" CA ALA D 77 " pdb=" CB ALA D 77 " ideal model delta sigma weight residual 1.536 1.419 0.117 2.53e-02 1.56e+03 2.13e+01 bond pdb=" CA ALA A 77 " pdb=" CB ALA A 77 " ideal model delta sigma weight residual 1.535 1.440 0.095 2.09e-02 2.29e+03 2.08e+01 bond pdb=" CE1 HIS C 20 " pdb=" NE2 HIS C 20 " ideal model delta sigma weight residual 1.321 1.366 -0.045 1.00e-02 1.00e+04 2.05e+01 ... (remaining 11302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 14315 3.48 - 6.96: 830 6.96 - 10.44: 92 10.44 - 13.92: 12 13.92 - 17.40: 1 Bond angle restraints: 15250 Sorted by residual: angle pdb=" C GLN B 86 " pdb=" CA GLN B 86 " pdb=" CB GLN B 86 " ideal model delta sigma weight residual 111.70 98.62 13.08 1.31e+00 5.83e-01 9.97e+01 angle pdb=" C GLN C 86 " pdb=" CA GLN C 86 " pdb=" CB GLN C 86 " ideal model delta sigma weight residual 111.70 99.23 12.47 1.31e+00 5.83e-01 9.07e+01 angle pdb=" C GLN E 86 " pdb=" CA GLN E 86 " pdb=" CB GLN E 86 " ideal model delta sigma weight residual 111.70 99.31 12.39 1.31e+00 5.83e-01 8.95e+01 angle pdb=" C GLN D 86 " pdb=" CA GLN D 86 " pdb=" CB GLN D 86 " ideal model delta sigma weight residual 111.51 98.84 12.67 1.38e+00 5.25e-01 8.43e+01 angle pdb=" CA THR B 202 " pdb=" CB THR B 202 " pdb=" OG1 THR B 202 " ideal model delta sigma weight residual 109.60 96.63 12.97 1.50e+00 4.44e-01 7.48e+01 ... (remaining 15245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 6255 35.66 - 71.31: 357 71.31 - 106.97: 29 106.97 - 142.63: 2 142.63 - 178.28: 5 Dihedral angle restraints: 6648 sinusoidal: 2818 harmonic: 3830 Sorted by residual: dihedral pdb=" C GLN D 109 " pdb=" N GLN D 109 " pdb=" CA GLN D 109 " pdb=" CB GLN D 109 " ideal model delta harmonic sigma weight residual -122.60 -135.66 13.06 0 2.50e+00 1.60e-01 2.73e+01 dihedral pdb=" C GLN B 86 " pdb=" N GLN B 86 " pdb=" CA GLN B 86 " pdb=" CB GLN B 86 " ideal model delta harmonic sigma weight residual -122.60 -109.56 -13.04 0 2.50e+00 1.60e-01 2.72e+01 dihedral pdb=" C GLN D 86 " pdb=" N GLN D 86 " pdb=" CA GLN D 86 " pdb=" CB GLN D 86 " ideal model delta harmonic sigma weight residual -122.60 -109.89 -12.71 0 2.50e+00 1.60e-01 2.58e+01 ... (remaining 6645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1100 0.100 - 0.200: 487 0.200 - 0.301: 92 0.301 - 0.401: 21 0.401 - 0.501: 5 Chirality restraints: 1705 Sorted by residual: chirality pdb=" CA GLN D 109 " pdb=" N GLN D 109 " pdb=" C GLN D 109 " pdb=" CB GLN D 109 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA GLN B 109 " pdb=" N GLN B 109 " pdb=" C GLN B 109 " pdb=" CB GLN B 109 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA GLN C 109 " pdb=" N GLN C 109 " pdb=" C GLN C 109 " pdb=" CB GLN C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.81e+00 ... (remaining 1702 not shown) Planarity restraints: 1775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 RET D 302 " -0.055 2.00e-02 2.50e+03 6.77e-02 5.73e+01 pdb=" C13 RET D 302 " 0.001 2.00e-02 2.50e+03 pdb=" C14 RET D 302 " 0.116 2.00e-02 2.50e+03 pdb=" C15 RET D 302 " -0.079 2.00e-02 2.50e+03 pdb=" C20 RET D 302 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET B 302 " 0.061 2.00e-02 2.50e+03 6.17e-02 4.76e+01 pdb=" C13 RET B 302 " -0.034 2.00e-02 2.50e+03 pdb=" C14 RET B 302 " -0.095 2.00e-02 2.50e+03 pdb=" C15 RET B 302 " 0.072 2.00e-02 2.50e+03 pdb=" C20 RET B 302 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET C 301 " 0.054 2.00e-02 2.50e+03 5.90e-02 4.35e+01 pdb=" C13 RET C 301 " -0.018 2.00e-02 2.50e+03 pdb=" C14 RET C 301 " -0.096 2.00e-02 2.50e+03 pdb=" C15 RET C 301 " 0.070 2.00e-02 2.50e+03 pdb=" C20 RET C 301 " -0.009 2.00e-02 2.50e+03 ... (remaining 1772 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 47 2.49 - 3.09: 8530 3.09 - 3.69: 17245 3.69 - 4.30: 27978 4.30 - 4.90: 45307 Nonbonded interactions: 99107 Sorted by model distance: nonbonded pdb=" O11 PC1 E 305 " pdb=" O32 PC1 E 305 " model vdw 1.883 3.040 nonbonded pdb=" OH TYR B 94 " pdb=" OD2 ASP C 19 " model vdw 2.124 3.040 nonbonded pdb=" O TYR A 76 " pdb=" O HOH A 401 " model vdw 2.155 3.040 nonbonded pdb=" OD2 ASP A 19 " pdb=" OH TYR E 94 " model vdw 2.181 3.040 nonbonded pdb=" OH TYR A 94 " pdb=" OD2 ASP B 19 " model vdw 2.186 3.040 ... (remaining 99102 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 263 or resid 303)) selection = (chain 'B' and (resid 1 through 263 or resid 303)) selection = (chain 'C' and (resid 1 through 263 or resid 303)) selection = (chain 'D' and (resid 1 through 263 or resid 303)) selection = (chain 'E' and (resid 1 through 263 or resid 303)) } 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.180 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 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 : 0.014 0.181 11312 Z= 0.890 Angle : 1.847 17.398 15250 Z= 1.169 Chirality : 0.112 0.501 1705 Planarity : 0.016 0.233 1775 Dihedral : 20.661 178.284 4198 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.81 % Allowed : 6.48 % Favored : 88.70 % Cbeta Deviations : 1.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.19), residues: 1305 helix: -1.91 (0.13), residues: 1005 sheet: None (None), residues: 0 loop : -1.02 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.009 ARG C 95 TYR 0.080 0.013 TYR E 238 PHE 0.044 0.010 PHE D 17 TRP 0.060 0.014 TRP E 201 HIS 0.031 0.013 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.01375 / 0.82 (11307) covalent geometry : angle 1.84718 / 1.17 (15250) hydrogen bonds : bond 0.20584 / 13.45 ( 846) hydrogen bonds : angle 8.22179 / 5.96 ( 2508) Misc. bond : bond 0.16974 / 8.77 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9415 (t0) cc_final: 0.9147 (t0) REVERT: A 79 VAL cc_start: 0.9602 (OUTLIER) cc_final: 0.9199 (p) REVERT: A 100 MET cc_start: 0.9386 (mmm) cc_final: 0.9011 (mmm) REVERT: A 117 LYS cc_start: 0.9540 (ptpp) cc_final: 0.9263 (pmmt) REVERT: A 149 ASP cc_start: 0.9373 (t0) cc_final: 0.9086 (t0) REVERT: B 19 ASP cc_start: 0.9490 (t0) cc_final: 0.9119 (t0) REVERT: B 79 VAL cc_start: 0.9564 (OUTLIER) cc_final: 0.9023 (m) REVERT: B 80 ASP cc_start: 0.9533 (m-30) cc_final: 0.9304 (p0) REVERT: B 98 ASN cc_start: 0.9398 (t0) cc_final: 0.9028 (t0) REVERT: B 149 ASP cc_start: 0.9485 (t0) cc_final: 0.9112 (t0) REVERT: C 19 ASP cc_start: 0.9412 (t0) cc_final: 0.9012 (t70) REVERT: C 79 VAL cc_start: 0.9611 (OUTLIER) cc_final: 0.9114 (m) REVERT: C 80 ASP cc_start: 0.9596 (m-30) cc_final: 0.9287 (p0) REVERT: D 79 VAL cc_start: 0.9629 (OUTLIER) cc_final: 0.9101 (m) REVERT: D 149 ASP cc_start: 0.9225 (t0) cc_final: 0.8875 (t0) REVERT: D 179 ARG cc_start: 0.9064 (ttp-170) cc_final: 0.8835 (ttp80) REVERT: E 5 GLU cc_start: 0.9407 (mp0) cc_final: 0.9177 (mp0) REVERT: E 79 VAL cc_start: 0.9542 (OUTLIER) cc_final: 0.8996 (m) REVERT: E 98 ASN cc_start: 0.9455 (t0) cc_final: 0.9022 (t0) outliers start: 52 outliers final: 10 residues processed: 243 average time/residue: 0.4787 time to fit residues: 126.4613 Evaluate side-chains 201 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 188 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 ASN A 14 GLN A 20 HIS A 41 GLN A 68 GLN A 98 ASN A 109 GLN A 215 ASN B 3 ASN B 68 GLN B 84 GLN B 215 ASN B 248 GLN B 260 GLN C 3 ASN C 41 GLN C 109 GLN C 215 ASN C 259 GLN D 29 HIS D 92 ASN D 215 ASN D 248 GLN D 259 GLN E 41 GLN E 84 GLN E 92 ASN E 248 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.065406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.053046 restraints weight = 30280.705| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 2.72 r_work: 0.2523 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11312 Z= 0.187 Angle : 0.637 7.742 15250 Z= 0.346 Chirality : 0.042 0.157 1705 Planarity : 0.005 0.043 1775 Dihedral : 19.785 171.935 2040 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.31 % Allowed : 14.91 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.22), residues: 1305 helix: 1.62 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 0.18 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 95 TYR 0.016 0.002 TYR B 255 PHE 0.014 0.002 PHE A 199 TRP 0.011 0.001 TRP E 201 HIS 0.002 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (11307) covalent geometry : angle 0.63677 / 0.35 (15250) hydrogen bonds : bond 0.07255 / 4.71 ( 846) hydrogen bonds : angle 4.68367 / 3.42 ( 2508) Misc. bond : bond 0.00173 / 0.09 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.340 Fit side-chains REVERT: A 5 GLU cc_start: 0.9215 (mp0) cc_final: 0.8878 (mp0) REVERT: A 46 LYS cc_start: 0.9597 (ttmm) cc_final: 0.9062 (ttpp) REVERT: A 100 MET cc_start: 0.9510 (mmm) cc_final: 0.8606 (mmm) REVERT: A 149 ASP cc_start: 0.8551 (t0) cc_final: 0.8139 (t0) REVERT: B 5 GLU cc_start: 0.9280 (mp0) cc_final: 0.9016 (mp0) REVERT: B 79 VAL cc_start: 0.9338 (OUTLIER) cc_final: 0.8533 (m) REVERT: B 98 ASN cc_start: 0.9365 (t0) cc_final: 0.8911 (t0) REVERT: B 149 ASP cc_start: 0.8923 (t0) cc_final: 0.8301 (t0) REVERT: B 214 MET cc_start: 0.8628 (mtp) cc_final: 0.8236 (ttm) REVERT: C 5 GLU cc_start: 0.9126 (mp0) cc_final: 0.8716 (mp0) REVERT: C 19 ASP cc_start: 0.9467 (t0) cc_final: 0.9191 (t70) REVERT: C 79 VAL cc_start: 0.9484 (OUTLIER) cc_final: 0.8805 (p) REVERT: C 98 ASN cc_start: 0.9286 (t0) cc_final: 0.8752 (t0) REVERT: C 214 MET cc_start: 0.8808 (mtp) cc_final: 0.8570 (mtp) REVERT: D 5 GLU cc_start: 0.9228 (mp0) cc_final: 0.8876 (mp0) REVERT: D 149 ASP cc_start: 0.8501 (t0) cc_final: 0.8061 (t0) REVERT: D 179 ARG cc_start: 0.9184 (ttp-170) cc_final: 0.8791 (ttp-110) REVERT: D 214 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8837 (ttp) REVERT: E 5 GLU cc_start: 0.9250 (mp0) cc_final: 0.8704 (mp0) REVERT: E 9 ASP cc_start: 0.8704 (m-30) cc_final: 0.8463 (m-30) REVERT: E 98 ASN cc_start: 0.9302 (t0) cc_final: 0.8672 (t0) REVERT: E 100 MET cc_start: 0.9579 (mmm) cc_final: 0.8610 (mmm) REVERT: E 117 LYS cc_start: 0.8870 (pmmt) cc_final: 0.8412 (mtmm) outliers start: 25 outliers final: 6 residues processed: 218 average time/residue: 0.4922 time to fit residues: 116.6224 Evaluate side-chains 195 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 101 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 HIS A 41 GLN A 98 ASN A 115 ASN B 3 ASN C 20 HIS C 41 GLN E 20 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.065934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.053620 restraints weight = 30192.877| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 2.77 r_work: 0.2555 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11312 Z= 0.163 Angle : 0.587 7.318 15250 Z= 0.312 Chirality : 0.039 0.165 1705 Planarity : 0.004 0.056 1775 Dihedral : 17.811 169.833 2029 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.04 % Allowed : 16.30 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.33 (0.22), residues: 1305 helix: 2.67 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 0.54 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 179 TYR 0.012 0.001 TYR B 238 PHE 0.008 0.001 PHE C 36 TRP 0.006 0.001 TRP B 169 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (11307) covalent geometry : angle 0.58656 / 0.31 (15250) hydrogen bonds : bond 0.06210 / 4.04 ( 846) hydrogen bonds : angle 4.28115 / 3.12 ( 2508) Misc. bond : bond 0.00030 / 0.02 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.412 Fit side-chains REVERT: A 3 ASN cc_start: 0.9278 (m-40) cc_final: 0.8682 (OUTLIER) REVERT: A 5 GLU cc_start: 0.9243 (mp0) cc_final: 0.9015 (mp0) REVERT: A 9 ASP cc_start: 0.8895 (m-30) cc_final: 0.8667 (m-30) REVERT: A 100 MET cc_start: 0.9407 (mmm) cc_final: 0.8680 (mmm) REVERT: A 149 ASP cc_start: 0.8498 (t0) cc_final: 0.8145 (t0) REVERT: B 19 ASP cc_start: 0.9470 (t70) cc_final: 0.9246 (t0) REVERT: B 98 ASN cc_start: 0.9379 (t0) cc_final: 0.8919 (t0) REVERT: B 149 ASP cc_start: 0.8860 (t0) cc_final: 0.8243 (t0) REVERT: B 214 MET cc_start: 0.8844 (mtp) cc_final: 0.8555 (ttm) REVERT: C 5 GLU cc_start: 0.9148 (mp0) cc_final: 0.8773 (mp0) REVERT: C 19 ASP cc_start: 0.9444 (t0) cc_final: 0.9108 (t70) REVERT: C 98 ASN cc_start: 0.9273 (t0) cc_final: 0.8742 (t0) REVERT: C 214 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8611 (ttt) REVERT: D 5 GLU cc_start: 0.9315 (mp0) cc_final: 0.9039 (mp0) REVERT: D 149 ASP cc_start: 0.8505 (t0) cc_final: 0.8111 (t0) REVERT: D 168 ASN cc_start: 0.9064 (t0) cc_final: 0.8743 (t0) REVERT: D 179 ARG cc_start: 0.9274 (ttp-170) cc_final: 0.8894 (ttp-110) REVERT: D 214 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8899 (ttp) REVERT: E 5 GLU cc_start: 0.9256 (mp0) cc_final: 0.8654 (mp0) REVERT: E 9 ASP cc_start: 0.8777 (m-30) cc_final: 0.8531 (m-30) REVERT: E 98 ASN cc_start: 0.9302 (t0) cc_final: 0.8735 (t0) REVERT: E 100 MET cc_start: 0.9499 (mmm) cc_final: 0.9187 (mmm) outliers start: 22 outliers final: 9 residues processed: 219 average time/residue: 0.4923 time to fit residues: 117.0243 Evaluate side-chains 196 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 167 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 58 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN A 98 ASN B 3 ASN C 41 GLN C 84 GLN E 115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.067006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.054810 restraints weight = 30104.257| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.79 r_work: 0.2552 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11312 Z= 0.172 Angle : 0.599 7.505 15250 Z= 0.315 Chirality : 0.039 0.169 1705 Planarity : 0.004 0.036 1775 Dihedral : 16.707 169.851 2027 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.76 % Allowed : 17.50 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.59 (0.22), residues: 1305 helix: 2.91 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 0.39 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 179 TYR 0.011 0.001 TYR B 238 PHE 0.007 0.001 PHE B 199 TRP 0.005 0.001 TRP D 72 HIS 0.003 0.001 HIS E 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (11307) covalent geometry : angle 0.59870 / 0.31 (15250) hydrogen bonds : bond 0.05946 / 3.86 ( 846) hydrogen bonds : angle 4.15854 / 3.03 ( 2508) Misc. bond : bond 0.00032 / 0.02 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 0.423 Fit side-chains REVERT: A 3 ASN cc_start: 0.9355 (m-40) cc_final: 0.8393 (OUTLIER) REVERT: A 5 GLU cc_start: 0.9218 (mp0) cc_final: 0.8988 (mp0) REVERT: A 9 ASP cc_start: 0.8941 (m-30) cc_final: 0.8735 (m-30) REVERT: A 98 ASN cc_start: 0.9360 (t0) cc_final: 0.9100 (t0) REVERT: A 100 MET cc_start: 0.9418 (mmm) cc_final: 0.8691 (mmm) REVERT: A 149 ASP cc_start: 0.8554 (t0) cc_final: 0.8242 (t0) REVERT: A 214 MET cc_start: 0.9230 (ttm) cc_final: 0.8835 (ttp) REVERT: B 98 ASN cc_start: 0.9355 (t0) cc_final: 0.8806 (t0) REVERT: B 120 GLU cc_start: 0.8716 (pm20) cc_final: 0.8511 (pm20) REVERT: B 149 ASP cc_start: 0.8936 (t0) cc_final: 0.8399 (t0) REVERT: B 214 MET cc_start: 0.8860 (mtp) cc_final: 0.8470 (ttm) REVERT: C 5 GLU cc_start: 0.9136 (mp0) cc_final: 0.8750 (mp0) REVERT: C 19 ASP cc_start: 0.9451 (t0) cc_final: 0.9086 (t70) REVERT: C 98 ASN cc_start: 0.9272 (t0) cc_final: 0.8754 (t0) REVERT: C 214 MET cc_start: 0.8967 (mtp) cc_final: 0.8558 (ttt) REVERT: D 5 GLU cc_start: 0.9277 (mp0) cc_final: 0.9004 (mp0) REVERT: D 146 GLU cc_start: 0.8704 (pt0) cc_final: 0.8331 (pp20) REVERT: D 149 ASP cc_start: 0.8505 (t0) cc_final: 0.7986 (t0) REVERT: D 168 ASN cc_start: 0.9066 (t0) cc_final: 0.8796 (t0) REVERT: D 179 ARG cc_start: 0.9311 (ttp-170) cc_final: 0.8931 (ttp-110) REVERT: D 214 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8840 (ttp) REVERT: E 5 GLU cc_start: 0.9193 (mp0) cc_final: 0.8551 (mp0) REVERT: E 98 ASN cc_start: 0.9277 (t0) cc_final: 0.8741 (t0) REVERT: E 100 MET cc_start: 0.9480 (mmm) cc_final: 0.9156 (mmm) outliers start: 19 outliers final: 11 residues processed: 206 average time/residue: 0.5540 time to fit residues: 123.5334 Evaluate side-chains 189 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 167 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 38 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 ASN A 41 GLN C 41 GLN D 115 ASN D 249 GLN E 98 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.067715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.055894 restraints weight = 29865.165| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 2.75 r_work: 0.2560 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11312 Z= 0.164 Angle : 0.613 7.741 15250 Z= 0.318 Chirality : 0.039 0.171 1705 Planarity : 0.004 0.038 1775 Dihedral : 15.889 170.257 2027 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.67 % Allowed : 18.80 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.23), residues: 1305 helix: 3.00 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 0.32 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 179 TYR 0.010 0.001 TYR A 208 PHE 0.007 0.001 PHE A 164 TRP 0.004 0.001 TRP D 133 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (11307) covalent geometry : angle 0.61349 / 0.32 (15250) hydrogen bonds : bond 0.05698 / 3.70 ( 846) hydrogen bonds : angle 4.05784 / 2.95 ( 2508) Misc. bond : bond 0.00023 / 0.01 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.444 Fit side-chains REVERT: A 5 GLU cc_start: 0.9176 (mp0) cc_final: 0.8950 (mp0) REVERT: A 9 ASP cc_start: 0.8934 (m-30) cc_final: 0.8716 (m-30) REVERT: A 100 MET cc_start: 0.9413 (mmm) cc_final: 0.8681 (mmm) REVERT: A 120 GLU cc_start: 0.8917 (pm20) cc_final: 0.8698 (pm20) REVERT: A 149 ASP cc_start: 0.8613 (t0) cc_final: 0.8333 (t0) REVERT: B 98 ASN cc_start: 0.9340 (t0) cc_final: 0.8784 (t0) REVERT: B 149 ASP cc_start: 0.8984 (t0) cc_final: 0.8470 (t0) REVERT: B 214 MET cc_start: 0.8925 (mtp) cc_final: 0.8550 (ttm) REVERT: C 5 GLU cc_start: 0.9113 (mp0) cc_final: 0.8616 (mp0) REVERT: C 19 ASP cc_start: 0.9424 (t0) cc_final: 0.9056 (t70) REVERT: C 98 ASN cc_start: 0.9251 (t0) cc_final: 0.8716 (t0) REVERT: C 179 ARG cc_start: 0.9371 (ttp-110) cc_final: 0.9165 (ttp-110) REVERT: C 214 MET cc_start: 0.9016 (mtp) cc_final: 0.8670 (ttt) REVERT: D 5 GLU cc_start: 0.9248 (mp0) cc_final: 0.8971 (mp0) REVERT: D 146 GLU cc_start: 0.8633 (pt0) cc_final: 0.8387 (pp20) REVERT: D 149 ASP cc_start: 0.8516 (t0) cc_final: 0.8021 (t0) REVERT: D 168 ASN cc_start: 0.9083 (t0) cc_final: 0.8824 (t0) REVERT: D 179 ARG cc_start: 0.9336 (ttp-170) cc_final: 0.8938 (ttp-110) REVERT: D 214 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8886 (ttp) REVERT: E 5 GLU cc_start: 0.9178 (mp0) cc_final: 0.8567 (mp0) REVERT: E 55 CYS cc_start: 0.9381 (m) cc_final: 0.9131 (m) REVERT: E 98 ASN cc_start: 0.9228 (t0) cc_final: 0.8738 (t0) REVERT: E 100 MET cc_start: 0.9444 (mmm) cc_final: 0.8973 (mmm) outliers start: 18 outliers final: 10 residues processed: 203 average time/residue: 0.5431 time to fit residues: 119.4487 Evaluate side-chains 192 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 181 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 167 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 92 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN A 98 ASN E 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.067130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.054890 restraints weight = 30126.744| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.81 r_work: 0.2557 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11312 Z= 0.162 Angle : 0.619 8.793 15250 Z= 0.320 Chirality : 0.039 0.167 1705 Planarity : 0.004 0.037 1775 Dihedral : 15.195 170.871 2027 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.04 % Allowed : 19.44 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.74 (0.23), residues: 1305 helix: 3.05 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 0.30 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 179 TYR 0.010 0.001 TYR A 208 PHE 0.007 0.001 PHE B 199 TRP 0.005 0.001 TRP A 127 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (11307) covalent geometry : angle 0.61936 / 0.32 (15250) hydrogen bonds : bond 0.05589 / 3.63 ( 846) hydrogen bonds : angle 4.01060 / 2.92 ( 2508) Misc. bond : bond 0.00026 / 0.01 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.487 Fit side-chains REVERT: A 5 GLU cc_start: 0.9176 (mp0) cc_final: 0.8934 (mp0) REVERT: A 98 ASN cc_start: 0.9334 (t0) cc_final: 0.9069 (t0) REVERT: A 100 MET cc_start: 0.9412 (mmm) cc_final: 0.8882 (mmm) REVERT: A 149 ASP cc_start: 0.8672 (t0) cc_final: 0.8362 (t0) REVERT: A 177 LYS cc_start: 0.9202 (ttpp) cc_final: 0.8864 (tmmm) REVERT: A 179 ARG cc_start: 0.9208 (ttp80) cc_final: 0.8939 (ttp-110) REVERT: B 98 ASN cc_start: 0.9315 (t0) cc_final: 0.8825 (t0) REVERT: B 149 ASP cc_start: 0.8987 (t0) cc_final: 0.8479 (t0) REVERT: B 214 MET cc_start: 0.8914 (mtp) cc_final: 0.8517 (ttm) REVERT: C 5 GLU cc_start: 0.9155 (mp0) cc_final: 0.8771 (mp0) REVERT: C 19 ASP cc_start: 0.9416 (t0) cc_final: 0.9049 (t70) REVERT: C 98 ASN cc_start: 0.9247 (t0) cc_final: 0.8716 (t0) REVERT: C 179 ARG cc_start: 0.9412 (ttp-110) cc_final: 0.9202 (ttp-110) REVERT: C 214 MET cc_start: 0.9000 (mtp) cc_final: 0.8631 (ttt) REVERT: D 5 GLU cc_start: 0.9231 (mp0) cc_final: 0.8978 (mp0) REVERT: D 146 GLU cc_start: 0.8648 (pt0) cc_final: 0.8439 (pp20) REVERT: D 149 ASP cc_start: 0.8547 (t0) cc_final: 0.8078 (t0) REVERT: D 168 ASN cc_start: 0.9084 (t0) cc_final: 0.8847 (t0) REVERT: D 179 ARG cc_start: 0.9388 (ttp-170) cc_final: 0.8943 (ttp-110) REVERT: E 5 GLU cc_start: 0.9159 (mp0) cc_final: 0.8694 (mp0) REVERT: E 98 ASN cc_start: 0.9246 (t0) cc_final: 0.8706 (t0) REVERT: E 100 MET cc_start: 0.9421 (mmm) cc_final: 0.8987 (mmm) outliers start: 22 outliers final: 11 residues processed: 207 average time/residue: 0.5754 time to fit residues: 129.1611 Evaluate side-chains 197 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 210 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 19 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 120 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN D 109 GLN E 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.066222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.054109 restraints weight = 30265.810| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.78 r_work: 0.2539 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11312 Z= 0.174 Angle : 0.659 8.741 15250 Z= 0.336 Chirality : 0.039 0.169 1705 Planarity : 0.004 0.030 1775 Dihedral : 14.819 171.323 2025 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.85 % Allowed : 20.00 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.79 (0.23), residues: 1305 helix: 3.09 (0.16), residues: 1015 sheet: None (None), residues: 0 loop : 0.30 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 179 TYR 0.010 0.001 TYR A 208 PHE 0.008 0.001 PHE B 199 TRP 0.005 0.001 TRP D 133 HIS 0.002 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (11307) covalent geometry : angle 0.65902 / 0.34 (15250) hydrogen bonds : bond 0.05597 / 3.64 ( 846) hydrogen bonds : angle 3.99908 / 2.91 ( 2508) Misc. bond : bond 0.00036 / 0.02 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.419 Fit side-chains REVERT: A 5 GLU cc_start: 0.9155 (mp0) cc_final: 0.8931 (mp0) REVERT: A 100 MET cc_start: 0.9456 (mmm) cc_final: 0.8911 (mmm) REVERT: A 149 ASP cc_start: 0.8675 (t0) cc_final: 0.8375 (t0) REVERT: A 174 LYS cc_start: 0.9364 (mmtt) cc_final: 0.9129 (mptp) REVERT: A 177 LYS cc_start: 0.9255 (ttpp) cc_final: 0.8974 (tmmm) REVERT: A 179 ARG cc_start: 0.9234 (ttp80) cc_final: 0.8924 (ttp-110) REVERT: B 98 ASN cc_start: 0.9323 (t0) cc_final: 0.8808 (t0) REVERT: B 100 MET cc_start: 0.9650 (mmm) cc_final: 0.9284 (mmm) REVERT: B 149 ASP cc_start: 0.9030 (t0) cc_final: 0.8565 (t0) REVERT: B 214 MET cc_start: 0.8963 (mtp) cc_final: 0.8608 (ttm) REVERT: C 5 GLU cc_start: 0.9134 (mp0) cc_final: 0.8747 (mp0) REVERT: C 19 ASP cc_start: 0.9417 (t0) cc_final: 0.9048 (t70) REVERT: C 98 ASN cc_start: 0.9272 (t0) cc_final: 0.8748 (t0) REVERT: C 179 ARG cc_start: 0.9375 (ttp-110) cc_final: 0.9174 (ttp-110) REVERT: C 214 MET cc_start: 0.9056 (mtp) cc_final: 0.8705 (ttt) REVERT: C 233 SER cc_start: 0.9702 (m) cc_final: 0.9477 (p) REVERT: D 5 GLU cc_start: 0.9238 (mp0) cc_final: 0.8969 (mp0) REVERT: D 146 GLU cc_start: 0.8649 (pt0) cc_final: 0.8403 (pp20) REVERT: D 149 ASP cc_start: 0.8572 (t0) cc_final: 0.8107 (t0) REVERT: D 168 ASN cc_start: 0.9087 (t0) cc_final: 0.8867 (t0) REVERT: D 179 ARG cc_start: 0.9347 (ttp-170) cc_final: 0.8907 (ttp-110) REVERT: D 214 MET cc_start: 0.9121 (ttm) cc_final: 0.8783 (ttp) REVERT: E 5 GLU cc_start: 0.9160 (mp0) cc_final: 0.8767 (mp0) REVERT: E 98 ASN cc_start: 0.9250 (t0) cc_final: 0.8784 (t0) REVERT: E 100 MET cc_start: 0.9465 (mmm) cc_final: 0.9034 (mmm) REVERT: E 146 GLU cc_start: 0.8628 (pp20) cc_final: 0.8168 (pp20) outliers start: 20 outliers final: 13 residues processed: 209 average time/residue: 0.5788 time to fit residues: 131.1030 Evaluate side-chains 202 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 174 LYS Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 210 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 82 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN A 98 ASN C 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.068031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.055883 restraints weight = 30109.400| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.82 r_work: 0.2581 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11312 Z= 0.144 Angle : 0.654 9.772 15250 Z= 0.332 Chirality : 0.039 0.184 1705 Planarity : 0.004 0.032 1775 Dihedral : 14.174 171.221 2025 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.30 % Allowed : 21.67 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.83 (0.23), residues: 1305 helix: 3.12 (0.16), residues: 1015 sheet: None (None), residues: 0 loop : 0.31 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 179 TYR 0.010 0.001 TYR A 208 PHE 0.007 0.001 PHE B 199 TRP 0.008 0.001 TRP D 133 HIS 0.003 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (11307) covalent geometry : angle 0.65361 / 0.33 (15250) hydrogen bonds : bond 0.05116 / 3.32 ( 846) hydrogen bonds : angle 3.90435 / 2.83 ( 2508) Misc. bond : bond 0.00010 / 0.01 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 215 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9135 (mp0) cc_final: 0.8855 (mp0) REVERT: A 98 ASN cc_start: 0.9328 (t0) cc_final: 0.8996 (t0) REVERT: A 100 MET cc_start: 0.9435 (mmm) cc_final: 0.8614 (mmm) REVERT: A 149 ASP cc_start: 0.8622 (t0) cc_final: 0.8334 (t0) REVERT: A 174 LYS cc_start: 0.9365 (mmtt) cc_final: 0.9157 (mptp) REVERT: A 177 LYS cc_start: 0.9288 (ttpp) cc_final: 0.9012 (tmmm) REVERT: A 179 ARG cc_start: 0.9220 (ttp80) cc_final: 0.8952 (ttp-110) REVERT: B 98 ASN cc_start: 0.9296 (t0) cc_final: 0.8846 (t0) REVERT: B 100 MET cc_start: 0.9591 (mmm) cc_final: 0.9265 (mmm) REVERT: B 149 ASP cc_start: 0.8980 (t0) cc_final: 0.8504 (t0) REVERT: B 214 MET cc_start: 0.8898 (mtp) cc_final: 0.8571 (ttm) REVERT: C 5 GLU cc_start: 0.9109 (mp0) cc_final: 0.8735 (mp0) REVERT: C 19 ASP cc_start: 0.9383 (t0) cc_final: 0.9009 (t70) REVERT: C 214 MET cc_start: 0.8986 (mtp) cc_final: 0.8544 (ttt) REVERT: C 233 SER cc_start: 0.9694 (m) cc_final: 0.9477 (p) REVERT: D 5 GLU cc_start: 0.9234 (mp0) cc_final: 0.8877 (mp0) REVERT: D 149 ASP cc_start: 0.8543 (t0) cc_final: 0.8069 (t0) REVERT: D 168 ASN cc_start: 0.9061 (t0) cc_final: 0.8828 (t0) REVERT: D 179 ARG cc_start: 0.9314 (ttp-170) cc_final: 0.8891 (ttp-110) REVERT: D 214 MET cc_start: 0.9045 (ttm) cc_final: 0.8787 (ttp) REVERT: E 5 GLU cc_start: 0.9110 (mp0) cc_final: 0.8756 (mp0) REVERT: E 98 ASN cc_start: 0.9210 (t0) cc_final: 0.8718 (t0) REVERT: E 146 GLU cc_start: 0.8642 (pp20) cc_final: 0.8276 (pp20) REVERT: E 149 ASP cc_start: 0.8671 (t0) cc_final: 0.7621 (p0) REVERT: E 179 ARG cc_start: 0.9116 (ttp-110) cc_final: 0.8879 (ttp-110) outliers start: 14 outliers final: 9 residues processed: 221 average time/residue: 0.5862 time to fit residues: 140.3063 Evaluate side-chains 212 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 174 LYS Chi-restraints excluded: chain E residue 210 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 54 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN D 109 GLN E 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.065351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.053192 restraints weight = 30321.293| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 2.78 r_work: 0.2526 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11312 Z= 0.206 Angle : 0.694 9.957 15250 Z= 0.353 Chirality : 0.041 0.180 1705 Planarity : 0.004 0.040 1775 Dihedral : 13.987 171.008 2023 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.02 % Allowed : 23.15 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.83 (0.23), residues: 1305 helix: 3.12 (0.16), residues: 1015 sheet: None (None), residues: 0 loop : 0.29 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 95 TYR 0.009 0.001 TYR A 208 PHE 0.026 0.001 PHE D 199 TRP 0.008 0.001 TRP E 133 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (11307) covalent geometry : angle 0.69374 / 0.35 (15250) hydrogen bonds : bond 0.05629 / 3.65 ( 846) hydrogen bonds : angle 4.02036 / 2.92 ( 2508) Misc. bond : bond 0.00057 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9154 (mp0) cc_final: 0.8941 (mp0) REVERT: A 98 ASN cc_start: 0.9319 (t0) cc_final: 0.9067 (t0) REVERT: A 100 MET cc_start: 0.9488 (mmm) cc_final: 0.8682 (mmm) REVERT: A 149 ASP cc_start: 0.8681 (t0) cc_final: 0.8387 (t0) REVERT: A 174 LYS cc_start: 0.9452 (mmtt) cc_final: 0.9233 (mptp) REVERT: A 177 LYS cc_start: 0.9333 (ttpp) cc_final: 0.9029 (tmmm) REVERT: B 98 ASN cc_start: 0.9316 (t0) cc_final: 0.8848 (t0) REVERT: B 149 ASP cc_start: 0.9035 (t0) cc_final: 0.8567 (t0) REVERT: B 214 MET cc_start: 0.9018 (mtp) cc_final: 0.8676 (ttm) REVERT: C 5 GLU cc_start: 0.9119 (mp0) cc_final: 0.8709 (mp0) REVERT: C 19 ASP cc_start: 0.9400 (t0) cc_final: 0.9024 (t70) REVERT: C 98 ASN cc_start: 0.9270 (t0) cc_final: 0.8916 (t0) REVERT: C 214 MET cc_start: 0.9105 (mtp) cc_final: 0.8650 (ttm) REVERT: C 233 SER cc_start: 0.9693 (m) cc_final: 0.9482 (p) REVERT: D 149 ASP cc_start: 0.8595 (t0) cc_final: 0.8177 (t0) REVERT: D 168 ASN cc_start: 0.9042 (t0) cc_final: 0.8833 (t0) REVERT: D 179 ARG cc_start: 0.9365 (ttp-170) cc_final: 0.8937 (ttp-110) REVERT: D 214 MET cc_start: 0.9107 (ttm) cc_final: 0.8836 (ttp) REVERT: E 5 GLU cc_start: 0.9114 (mp0) cc_final: 0.8708 (mp0) REVERT: E 98 ASN cc_start: 0.9265 (t0) cc_final: 0.8720 (t0) REVERT: E 100 MET cc_start: 0.9751 (mmm) cc_final: 0.9295 (mmm) REVERT: E 146 GLU cc_start: 0.8651 (pp20) cc_final: 0.8296 (pp20) REVERT: E 179 ARG cc_start: 0.9173 (ttp-110) cc_final: 0.8932 (ttp-110) outliers start: 11 outliers final: 8 residues processed: 202 average time/residue: 0.5563 time to fit residues: 122.0708 Evaluate side-chains 200 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 192 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 210 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN D 98 ASN E 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.068061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.055933 restraints weight = 29952.889| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.81 r_work: 0.2593 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11312 Z= 0.146 Angle : 0.694 10.411 15250 Z= 0.352 Chirality : 0.040 0.192 1705 Planarity : 0.004 0.041 1775 Dihedral : 13.465 169.967 2023 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.02 % Allowed : 23.80 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.79 (0.23), residues: 1305 helix: 3.10 (0.16), residues: 1015 sheet: None (None), residues: 0 loop : 0.24 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 179 TYR 0.010 0.001 TYR A 208 PHE 0.025 0.001 PHE D 199 TRP 0.011 0.001 TRP D 133 HIS 0.003 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (11307) covalent geometry : angle 0.69418 / 0.35 (15250) hydrogen bonds : bond 0.05059 / 3.29 ( 846) hydrogen bonds : angle 3.89284 / 2.82 ( 2508) Misc. bond : bond 0.00015 / 0.01 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9138 (mp0) cc_final: 0.8930 (mp0) REVERT: A 98 ASN cc_start: 0.9270 (t0) cc_final: 0.8832 (t0) REVERT: A 149 ASP cc_start: 0.8657 (t0) cc_final: 0.8368 (t0) REVERT: A 174 LYS cc_start: 0.9429 (mmtt) cc_final: 0.9223 (mptp) REVERT: A 177 LYS cc_start: 0.9333 (ttpp) cc_final: 0.9060 (tmmm) REVERT: A 179 ARG cc_start: 0.9316 (ttp80) cc_final: 0.9040 (ttp-110) REVERT: A 214 MET cc_start: 0.9183 (ttm) cc_final: 0.8770 (ttp) REVERT: B 98 ASN cc_start: 0.9283 (t0) cc_final: 0.8823 (t0) REVERT: B 149 ASP cc_start: 0.8991 (t0) cc_final: 0.8533 (t0) REVERT: B 214 MET cc_start: 0.8916 (mtp) cc_final: 0.8544 (ttm) REVERT: C 5 GLU cc_start: 0.9087 (mp0) cc_final: 0.8712 (mp0) REVERT: C 19 ASP cc_start: 0.9373 (t0) cc_final: 0.8994 (t70) REVERT: C 98 ASN cc_start: 0.9178 (t0) cc_final: 0.8793 (t0) REVERT: C 214 MET cc_start: 0.8970 (mtp) cc_final: 0.8636 (ttm) REVERT: C 233 SER cc_start: 0.9696 (m) cc_final: 0.9483 (p) REVERT: D 149 ASP cc_start: 0.8546 (t0) cc_final: 0.8133 (t0) REVERT: D 179 ARG cc_start: 0.9308 (ttp-170) cc_final: 0.8862 (ttp-110) REVERT: D 214 MET cc_start: 0.9061 (ttm) cc_final: 0.8831 (ttp) REVERT: E 5 GLU cc_start: 0.9089 (mp0) cc_final: 0.8712 (mp0) REVERT: E 98 ASN cc_start: 0.9238 (t0) cc_final: 0.8770 (t0) REVERT: E 100 MET cc_start: 0.9727 (OUTLIER) cc_final: 0.9243 (mmm) REVERT: E 146 GLU cc_start: 0.8614 (pp20) cc_final: 0.8287 (pp20) REVERT: E 149 ASP cc_start: 0.8576 (t0) cc_final: 0.7685 (p0) REVERT: E 179 ARG cc_start: 0.9138 (ttp-110) cc_final: 0.8923 (ttp-110) outliers start: 11 outliers final: 9 residues processed: 214 average time/residue: 0.5409 time to fit residues: 126.0317 Evaluate side-chains 211 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 210 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 96 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN D 109 GLN E 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.066997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.054804 restraints weight = 30254.663| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 2.80 r_work: 0.2570 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11312 Z= 0.160 Angle : 0.692 10.258 15250 Z= 0.350 Chirality : 0.040 0.186 1705 Planarity : 0.004 0.034 1775 Dihedral : 13.232 169.490 2023 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.02 % Allowed : 23.89 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.65 (0.23), residues: 1305 helix: 2.89 (0.16), residues: 1045 sheet: None (None), residues: 0 loop : 0.34 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 179 TYR 0.009 0.001 TYR A 208 PHE 0.026 0.001 PHE D 199 TRP 0.012 0.001 TRP D 133 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (11307) covalent geometry : angle 0.69239 / 0.35 (15250) hydrogen bonds : bond 0.05157 / 3.35 ( 846) hydrogen bonds : angle 3.93788 / 2.85 ( 2508) Misc. bond : bond 0.00022 / 0.01 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3489.00 seconds wall clock time: 60 minutes 34.57 seconds (3634.57 seconds total)