Starting phenix.real_space_refine on Wed Sep 17 20:58:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jox_61688/09_2025/9jox_61688.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jox_61688/09_2025/9jox_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jox_61688/09_2025/9jox_61688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jox_61688/09_2025/9jox_61688.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jox_61688/09_2025/9jox_61688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jox_61688/09_2025/9jox_61688.map" } 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-2.0-5805/lib/python3.9/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, 188 Unusual residues: {' CL': 2, 'D12': 1, 'PC1': 1, 'PLC': 2, 'R16': 1, 'RET': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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, 166 Unusual residues: {' CL': 2, '8K6': 1, 'C14': 1, 'PC1': 1, 'PLC': 1, 'R16': 1, 'RET': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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, 136 Unusual residues: {' CL': 2, '8K6': 1, 'PC1': 1, 'PLC': 1, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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, 162 Unusual residues: {' CL': 2, 'D12': 1, 'PC1': 1, 'PLC': 1, 'R16': 2, 'RET': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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, 122 Unusual residues: {' CL': 2, 'C14': 1, 'PC1': 1, 'R16': 2, 'RET': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 3.11, per 1000 atoms: 0.28 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: 1.22 Conformation dependent library (CDL) restraints added in 535.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.36 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: 1.93 Time building geometry restraints manager: 1.54 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.500 Find NCS groups from input model: 0.260 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:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 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 aren 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 covalent geometry : bond 0.01375 (11307) covalent geometry : angle 1.84718 (15250) hydrogen bonds : bond 0.20584 ( 846) hydrogen bonds : angle 8.22179 ( 2508) Misc. bond : bond 0.16974 ( 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 : 0.466 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: 0.5833 time to fit residues: 153.5570 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 : 0.417 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 14 GLN A 20 HIS A 41 GLN A 68 GLN 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.066875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.054797 restraints weight = 30345.517| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 2.72 r_work: 0.2526 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.2448 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= 0.189 Angle : 0.636 7.724 15250 Z= 0.346 Chirality : 0.042 0.160 1705 Planarity : 0.005 0.042 1775 Dihedral : 19.756 171.800 2040 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.39 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 aren not related in a simple way. whole: 1.92 (0.22), residues: 1305 helix: 1.63 (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 0.004 0.001 ARG A 95 TYR 0.016 0.002 TYR B 255 PHE 0.013 0.002 PHE A 199 TRP 0.012 0.001 TRP E 201 HIS 0.002 0.001 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00387 (11307) covalent geometry : angle 0.63553 (15250) hydrogen bonds : bond 0.07218 ( 846) hydrogen bonds : angle 4.68166 ( 2508) Misc. bond : bond 0.00013 ( 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 231 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.452 Fit side-chains REVERT: A 5 GLU cc_start: 0.9214 (mp0) cc_final: 0.8882 (mp0) REVERT: A 46 LYS cc_start: 0.9589 (ttmm) cc_final: 0.9053 (ttpp) REVERT: A 100 MET cc_start: 0.9515 (mmm) cc_final: 0.8613 (mmm) REVERT: A 149 ASP cc_start: 0.8553 (t0) cc_final: 0.8143 (t0) REVERT: B 5 GLU cc_start: 0.9276 (mp0) cc_final: 0.9020 (mp0) REVERT: B 79 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.8523 (m) REVERT: B 98 ASN cc_start: 0.9363 (t0) cc_final: 0.8882 (t0) REVERT: B 149 ASP cc_start: 0.8930 (t0) cc_final: 0.8307 (t0) REVERT: B 214 MET cc_start: 0.8628 (mtp) cc_final: 0.8236 (ttm) REVERT: C 5 GLU cc_start: 0.9122 (mp0) cc_final: 0.8719 (mp0) REVERT: C 19 ASP cc_start: 0.9464 (t0) cc_final: 0.9188 (t70) REVERT: C 79 VAL cc_start: 0.9494 (OUTLIER) cc_final: 0.8801 (p) REVERT: C 98 ASN cc_start: 0.9272 (t0) cc_final: 0.8714 (t0) REVERT: C 214 MET cc_start: 0.8815 (mtp) cc_final: 0.8583 (mtp) REVERT: D 5 GLU cc_start: 0.9223 (mp0) cc_final: 0.8877 (mp0) REVERT: D 149 ASP cc_start: 0.8478 (t0) cc_final: 0.8037 (t0) REVERT: D 179 ARG cc_start: 0.9189 (ttp-170) cc_final: 0.8797 (ttp-110) REVERT: D 214 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8852 (ttp) REVERT: E 5 GLU cc_start: 0.9253 (mp0) cc_final: 0.8709 (mp0) REVERT: E 9 ASP cc_start: 0.8706 (m-30) cc_final: 0.8468 (m-30) REVERT: E 98 ASN cc_start: 0.9288 (t0) cc_final: 0.8670 (t0) REVERT: E 100 MET cc_start: 0.9579 (mmm) cc_final: 0.8615 (mmm) REVERT: E 117 LYS cc_start: 0.8883 (pmmt) cc_final: 0.8418 (mtmm) outliers start: 25 outliers final: 6 residues processed: 217 average time/residue: 0.5946 time to fit residues: 139.6602 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 : 0.453 ------------------------------------------------------------------------------- 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: 0.0970 chunk 33 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 20 HIS A 41 GLN A 98 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 = 0.3051 r_free = 0.3051 target = 0.067618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.055357 restraints weight = 29952.666| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.77 r_work: 0.2586 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11312 Z= 0.147 Angle : 0.578 7.311 15250 Z= 0.308 Chirality : 0.039 0.169 1705 Planarity : 0.004 0.062 1775 Dihedral : 17.541 169.351 2029 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.94 % Allowed : 16.20 % Favored : 81.85 % 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 aren not related in a simple way. whole: 3.40 (0.22), residues: 1305 helix: 2.72 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 0.56 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 179 TYR 0.012 0.001 TYR C 255 PHE 0.009 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 covalent geometry : bond 0.00290 (11307) covalent geometry : angle 0.57849 (15250) hydrogen bonds : bond 0.05802 ( 846) hydrogen bonds : angle 4.20070 ( 2508) Misc. bond : bond 0.00023 ( 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 243 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.421 Fit side-chains REVERT: A 3 ASN cc_start: 0.9274 (m110) cc_final: 0.8673 (OUTLIER) REVERT: A 5 GLU cc_start: 0.9251 (mp0) cc_final: 0.9050 (mp0) REVERT: A 9 ASP cc_start: 0.8888 (m-30) cc_final: 0.8681 (m-30) REVERT: A 100 MET cc_start: 0.9378 (mmm) cc_final: 0.8642 (mmm) REVERT: A 149 ASP cc_start: 0.8441 (t0) cc_final: 0.8092 (t0) REVERT: B 98 ASN cc_start: 0.9367 (t0) cc_final: 0.8800 (t0) REVERT: B 100 MET cc_start: 0.9562 (mmm) cc_final: 0.8616 (mmm) REVERT: B 149 ASP cc_start: 0.8807 (t0) cc_final: 0.8218 (t0) REVERT: B 214 MET cc_start: 0.8789 (mtp) cc_final: 0.8440 (ttm) REVERT: C 5 GLU cc_start: 0.9159 (mp0) cc_final: 0.8714 (mp0) REVERT: C 19 ASP cc_start: 0.9423 (t0) cc_final: 0.9068 (t70) REVERT: C 98 ASN cc_start: 0.9251 (t0) cc_final: 0.8710 (t0) REVERT: C 214 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8588 (ttt) REVERT: D 5 GLU cc_start: 0.9318 (mp0) cc_final: 0.9042 (mp0) REVERT: D 149 ASP cc_start: 0.8425 (t0) cc_final: 0.8022 (t0) REVERT: D 168 ASN cc_start: 0.9060 (t0) cc_final: 0.8748 (t0) REVERT: D 179 ARG cc_start: 0.9275 (ttp-170) cc_final: 0.8909 (ttp-110) REVERT: D 214 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8887 (ttp) REVERT: E 5 GLU cc_start: 0.9245 (mp0) cc_final: 0.8648 (mp0) REVERT: E 9 ASP cc_start: 0.8757 (m-30) cc_final: 0.8557 (m-30) REVERT: E 98 ASN cc_start: 0.9295 (t0) cc_final: 0.8690 (t0) REVERT: E 100 MET cc_start: 0.9474 (mmm) cc_final: 0.9178 (mmm) outliers start: 21 outliers final: 9 residues processed: 233 average time/residue: 0.5718 time to fit residues: 144.5354 Evaluate side-chains 205 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 187 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 98 ASN C 41 GLN C 84 GLN C 109 GLN D 109 GLN D 115 ASN E 115 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.066754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.054260 restraints weight = 29982.116| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 2.78 r_work: 0.2570 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.3306 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= 0.159 Angle : 0.600 7.428 15250 Z= 0.312 Chirality : 0.039 0.181 1705 Planarity : 0.004 0.031 1775 Dihedral : 16.620 169.550 2027 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.04 % Allowed : 18.06 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.65 (0.22), residues: 1305 helix: 2.96 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 0.38 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 179 TYR 0.011 0.001 TYR A 238 PHE 0.007 0.001 PHE C 199 TRP 0.004 0.001 TRP D 72 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00341 (11307) covalent geometry : angle 0.60042 (15250) hydrogen bonds : bond 0.05673 ( 846) hydrogen bonds : angle 4.10450 ( 2508) Misc. bond : bond 0.00022 ( 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 217 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.480 Fit side-chains REVERT: A 3 ASN cc_start: 0.9464 (m110) cc_final: 0.9122 (m-40) REVERT: A 5 GLU cc_start: 0.9239 (mp0) cc_final: 0.8985 (mp0) REVERT: A 9 ASP cc_start: 0.8930 (m-30) cc_final: 0.8723 (m-30) REVERT: A 98 ASN cc_start: 0.9353 (t0) cc_final: 0.9090 (t0) REVERT: A 100 MET cc_start: 0.9375 (mmm) cc_final: 0.8859 (mmm) REVERT: A 149 ASP cc_start: 0.8498 (t0) cc_final: 0.8188 (t0) REVERT: B 98 ASN cc_start: 0.9349 (t0) cc_final: 0.8779 (t0) REVERT: B 149 ASP cc_start: 0.8876 (t0) cc_final: 0.8332 (t0) REVERT: B 214 MET cc_start: 0.8800 (mtp) cc_final: 0.8416 (ttm) REVERT: C 5 GLU cc_start: 0.9189 (mp0) cc_final: 0.8804 (mp0) REVERT: C 19 ASP cc_start: 0.9433 (t0) cc_final: 0.9042 (t70) REVERT: C 98 ASN cc_start: 0.9268 (t0) cc_final: 0.8740 (t0) REVERT: C 214 MET cc_start: 0.8935 (mtp) cc_final: 0.8466 (ttt) REVERT: D 5 GLU cc_start: 0.9280 (mp0) cc_final: 0.9020 (mp0) REVERT: D 120 GLU cc_start: 0.8716 (pm20) cc_final: 0.8507 (pm20) REVERT: D 146 GLU cc_start: 0.8659 (pt0) cc_final: 0.8340 (pp20) REVERT: D 149 ASP cc_start: 0.8427 (t0) cc_final: 0.7899 (t0) REVERT: D 168 ASN cc_start: 0.9085 (t0) cc_final: 0.8816 (t0) REVERT: D 179 ARG cc_start: 0.9337 (ttp-170) cc_final: 0.8939 (ttp-110) REVERT: D 214 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8802 (ttp) REVERT: E 5 GLU cc_start: 0.9211 (mp0) cc_final: 0.8582 (mp0) REVERT: E 9 ASP cc_start: 0.8772 (m-30) cc_final: 0.8542 (m-30) REVERT: E 55 CYS cc_start: 0.9405 (m) cc_final: 0.9176 (m) REVERT: E 98 ASN cc_start: 0.9257 (t0) cc_final: 0.8717 (t0) REVERT: E 100 MET cc_start: 0.9438 (mmm) cc_final: 0.8935 (mmm) outliers start: 22 outliers final: 10 residues processed: 208 average time/residue: 0.5734 time to fit residues: 129.0019 Evaluate side-chains 195 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 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 37 LEU 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: 2.9990 chunk 57 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN C 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.065970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.053471 restraints weight = 30492.669| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.82 r_work: 0.2550 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.3458 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= 0.162 Angle : 0.613 7.537 15250 Z= 0.318 Chirality : 0.039 0.189 1705 Planarity : 0.004 0.042 1775 Dihedral : 15.768 169.960 2027 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.04 % Allowed : 18.80 % Favored : 79.17 % 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 aren not related in a simple way. whole: 3.74 (0.22), residues: 1305 helix: 3.04 (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 0.011 0.001 TYR A 208 PHE 0.007 0.001 PHE C 199 TRP 0.005 0.001 TRP E 72 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00353 (11307) covalent geometry : angle 0.61304 (15250) hydrogen bonds : bond 0.05571 ( 846) hydrogen bonds : angle 4.03482 ( 2508) Misc. bond : bond 0.00025 ( 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 215 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9227 (mp0) cc_final: 0.8977 (mp0) REVERT: A 9 ASP cc_start: 0.8943 (m-30) cc_final: 0.8690 (m-30) REVERT: A 100 MET cc_start: 0.9397 (mmm) cc_final: 0.8867 (mmm) REVERT: A 149 ASP cc_start: 0.8564 (t0) cc_final: 0.8279 (t0) REVERT: A 177 LYS cc_start: 0.9082 (tmmm) cc_final: 0.8868 (ttpp) REVERT: A 179 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8887 (ttp-110) REVERT: B 98 ASN cc_start: 0.9344 (t0) cc_final: 0.8754 (t0) REVERT: B 149 ASP cc_start: 0.8940 (t0) cc_final: 0.8427 (t0) REVERT: B 214 MET cc_start: 0.8880 (mtp) cc_final: 0.8520 (ttm) REVERT: C 5 GLU cc_start: 0.9204 (mp0) cc_final: 0.8778 (mp0) REVERT: C 19 ASP cc_start: 0.9425 (t0) cc_final: 0.9040 (t70) REVERT: C 98 ASN cc_start: 0.9256 (t0) cc_final: 0.8722 (t0) REVERT: C 179 ARG cc_start: 0.9358 (ttp-110) cc_final: 0.9151 (ttp-110) REVERT: C 214 MET cc_start: 0.9013 (mtp) cc_final: 0.8642 (ttt) REVERT: D 5 GLU cc_start: 0.9270 (mp0) cc_final: 0.8979 (mp0) REVERT: D 149 ASP cc_start: 0.8488 (t0) cc_final: 0.7997 (t0) REVERT: D 168 ASN cc_start: 0.9097 (t0) cc_final: 0.8842 (t0) REVERT: D 179 ARG cc_start: 0.9355 (ttp-170) cc_final: 0.8940 (ttp-110) REVERT: D 214 MET cc_start: 0.9239 (mtp) cc_final: 0.8856 (ttp) REVERT: E 5 GLU cc_start: 0.9232 (mp0) cc_final: 0.8705 (mp0) REVERT: E 9 ASP cc_start: 0.8835 (m-30) cc_final: 0.8631 (m-30) REVERT: E 98 ASN cc_start: 0.9224 (t0) cc_final: 0.8662 (t0) REVERT: E 100 MET cc_start: 0.9423 (mmm) cc_final: 0.8945 (mmm) outliers start: 22 outliers final: 10 residues processed: 207 average time/residue: 0.5722 time to fit residues: 128.2627 Evaluate side-chains 197 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 187 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 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 E residue 73 THR Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 210 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 92 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN A 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.066137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.053641 restraints weight = 30707.363| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.87 r_work: 0.2544 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.3593 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= 0.167 Angle : 0.629 8.856 15250 Z= 0.325 Chirality : 0.039 0.188 1705 Planarity : 0.004 0.031 1775 Dihedral : 15.165 170.538 2027 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.94 % Allowed : 19.17 % Favored : 78.89 % 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 aren not related in a simple way. whole: 3.77 (0.23), residues: 1305 helix: 3.06 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 0.35 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 179 TYR 0.009 0.001 TYR A 208 PHE 0.007 0.001 PHE B 199 TRP 0.004 0.001 TRP D 72 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00366 (11307) covalent geometry : angle 0.62941 (15250) hydrogen bonds : bond 0.05561 ( 846) hydrogen bonds : angle 3.99688 ( 2508) Misc. bond : bond 0.00031 ( 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 214 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.463 Fit side-chains REVERT: A 5 GLU cc_start: 0.9205 (mp0) cc_final: 0.8949 (mp0) REVERT: A 9 ASP cc_start: 0.8936 (m-30) cc_final: 0.8685 (m-30) REVERT: A 98 ASN cc_start: 0.9341 (t0) cc_final: 0.9096 (t0) REVERT: A 100 MET cc_start: 0.9432 (mmm) cc_final: 0.8898 (mmm) REVERT: A 149 ASP cc_start: 0.8643 (t0) cc_final: 0.8347 (t0) REVERT: A 179 ARG cc_start: 0.9209 (ttp80) cc_final: 0.8913 (ttp-110) REVERT: A 214 MET cc_start: 0.9200 (ttm) cc_final: 0.8789 (ttp) REVERT: B 98 ASN cc_start: 0.9320 (t0) cc_final: 0.8831 (t0) REVERT: B 100 MET cc_start: 0.9609 (mmm) cc_final: 0.9040 (mmm) REVERT: B 119 LYS cc_start: 0.9283 (mmmt) cc_final: 0.9030 (mmmt) REVERT: B 149 ASP cc_start: 0.8966 (t0) cc_final: 0.8457 (t0) REVERT: B 214 MET cc_start: 0.8878 (mtp) cc_final: 0.8495 (ttm) REVERT: C 5 GLU cc_start: 0.9202 (mp0) cc_final: 0.8778 (mp0) REVERT: C 19 ASP cc_start: 0.9438 (t0) cc_final: 0.9049 (t70) REVERT: C 98 ASN cc_start: 0.9258 (t0) cc_final: 0.8734 (t0) REVERT: C 179 ARG cc_start: 0.9408 (ttp-110) cc_final: 0.9195 (ttp-110) REVERT: C 214 MET cc_start: 0.8987 (mtp) cc_final: 0.8580 (ttt) REVERT: D 5 GLU cc_start: 0.9315 (mp0) cc_final: 0.9072 (mp0) REVERT: D 149 ASP cc_start: 0.8475 (t0) cc_final: 0.8011 (t0) REVERT: D 168 ASN cc_start: 0.9082 (t0) cc_final: 0.8858 (t0) REVERT: D 179 ARG cc_start: 0.9371 (ttp-170) cc_final: 0.8910 (ttp-110) REVERT: D 214 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8852 (ttp) REVERT: E 5 GLU cc_start: 0.9210 (mp0) cc_final: 0.8689 (mp0) REVERT: E 9 ASP cc_start: 0.8867 (m-30) cc_final: 0.8658 (m-30) REVERT: E 98 ASN cc_start: 0.9241 (t0) cc_final: 0.8665 (t0) REVERT: E 100 MET cc_start: 0.9432 (mmm) cc_final: 0.8986 (mmm) outliers start: 21 outliers final: 11 residues processed: 206 average time/residue: 0.5722 time to fit residues: 127.5172 Evaluate side-chains 194 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 210 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 210 VAL 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 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: 10.0000 chunk 72 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.067184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.054732 restraints weight = 29730.624| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 2.81 r_work: 0.2559 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.3669 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 : 0.656 8.647 15250 Z= 0.334 Chirality : 0.040 0.177 1705 Planarity : 0.004 0.029 1775 Dihedral : 14.607 170.991 2025 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.76 % Allowed : 20.46 % Favored : 77.78 % 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 aren not related in a simple way. whole: 3.82 (0.23), residues: 1305 helix: 3.10 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 0.37 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 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 E 72 HIS 0.002 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00384 (11307) covalent geometry : angle 0.65597 (15250) hydrogen bonds : bond 0.05612 ( 846) hydrogen bonds : angle 3.97816 ( 2508) Misc. bond : bond 0.00037 ( 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 218 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9160 (mp0) cc_final: 0.8928 (mp0) REVERT: A 9 ASP cc_start: 0.8983 (m-30) cc_final: 0.8773 (m-30) REVERT: A 98 ASN cc_start: 0.9306 (t0) cc_final: 0.8982 (t0) REVERT: A 100 MET cc_start: 0.9447 (mmm) cc_final: 0.8896 (mmm) REVERT: A 149 ASP cc_start: 0.8671 (t0) cc_final: 0.8366 (t0) REVERT: A 174 LYS cc_start: 0.9323 (mmtt) cc_final: 0.9104 (mptp) REVERT: A 179 ARG cc_start: 0.9238 (ttp80) cc_final: 0.8922 (ttp-110) REVERT: B 98 ASN cc_start: 0.9307 (t0) cc_final: 0.8752 (t0) REVERT: B 119 LYS cc_start: 0.9231 (mmmt) cc_final: 0.8969 (mmmt) REVERT: B 149 ASP cc_start: 0.8999 (t0) cc_final: 0.8524 (t0) REVERT: B 214 MET cc_start: 0.8970 (mtp) cc_final: 0.8575 (ttm) REVERT: C 5 GLU cc_start: 0.9151 (mp0) cc_final: 0.8760 (mp0) REVERT: C 19 ASP cc_start: 0.9421 (t0) cc_final: 0.9057 (t70) REVERT: C 98 ASN cc_start: 0.9261 (t0) cc_final: 0.8730 (t0) REVERT: C 214 MET cc_start: 0.9061 (mtp) cc_final: 0.8693 (ttt) REVERT: C 233 SER cc_start: 0.9702 (m) cc_final: 0.9468 (p) REVERT: D 5 GLU cc_start: 0.9297 (mp0) cc_final: 0.9038 (mp0) REVERT: D 149 ASP cc_start: 0.8565 (t0) cc_final: 0.8146 (t0) REVERT: E 5 GLU cc_start: 0.9156 (mp0) cc_final: 0.8684 (mp0) REVERT: E 98 ASN cc_start: 0.9247 (t0) cc_final: 0.8696 (t0) REVERT: E 100 MET cc_start: 0.9441 (mmm) cc_final: 0.8994 (mmm) outliers start: 19 outliers final: 11 residues processed: 209 average time/residue: 0.5750 time to fit residues: 129.9755 Evaluate side-chains 201 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 1 MET 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 E residue 73 THR 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: 4.9990 chunk 111 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.065725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.053246 restraints weight = 29866.533| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.81 r_work: 0.2562 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11312 Z= 0.162 Angle : 0.655 8.872 15250 Z= 0.334 Chirality : 0.039 0.177 1705 Planarity : 0.004 0.030 1775 Dihedral : 14.262 170.627 2025 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.57 % Allowed : 21.67 % Favored : 76.76 % 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 aren not related in a simple way. whole: 3.83 (0.23), residues: 1305 helix: 3.10 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 0.39 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 179 TYR 0.009 0.001 TYR A 208 PHE 0.008 0.001 PHE B 199 TRP 0.006 0.001 TRP D 133 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00356 (11307) covalent geometry : angle 0.65468 (15250) hydrogen bonds : bond 0.05472 ( 846) hydrogen bonds : angle 3.96141 ( 2508) Misc. bond : bond 0.00022 ( 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 217 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.412 Fit side-chains REVERT: A 5 GLU cc_start: 0.9157 (mp0) cc_final: 0.8951 (mp0) REVERT: A 9 ASP cc_start: 0.8989 (m-30) cc_final: 0.8775 (m-30) REVERT: A 98 ASN cc_start: 0.9300 (t0) cc_final: 0.8959 (t0) REVERT: A 100 MET cc_start: 0.9448 (mmm) cc_final: 0.8882 (mmm) REVERT: A 149 ASP cc_start: 0.8645 (t0) cc_final: 0.8347 (t0) REVERT: A 174 LYS cc_start: 0.9323 (mmtt) cc_final: 0.9107 (mptp) REVERT: B 98 ASN cc_start: 0.9290 (t0) cc_final: 0.8723 (t0) REVERT: B 119 LYS cc_start: 0.9228 (mmmt) cc_final: 0.8982 (mmmt) REVERT: B 149 ASP cc_start: 0.8993 (t0) cc_final: 0.8520 (t0) REVERT: B 214 MET cc_start: 0.8917 (mtp) cc_final: 0.8587 (ttm) REVERT: C 5 GLU cc_start: 0.9161 (mp0) cc_final: 0.8756 (mp0) REVERT: C 19 ASP cc_start: 0.9419 (t0) cc_final: 0.9028 (t70) REVERT: C 98 ASN cc_start: 0.9256 (t0) cc_final: 0.8724 (t0) REVERT: C 214 MET cc_start: 0.9017 (mtp) cc_final: 0.8594 (ttt) REVERT: C 233 SER cc_start: 0.9701 (m) cc_final: 0.9470 (p) REVERT: D 5 GLU cc_start: 0.9307 (mp0) cc_final: 0.9045 (mp0) REVERT: D 149 ASP cc_start: 0.8572 (t0) cc_final: 0.8159 (t0) REVERT: E 5 GLU cc_start: 0.9163 (mp0) cc_final: 0.8769 (mp0) REVERT: E 98 ASN cc_start: 0.9256 (t0) cc_final: 0.8692 (t0) REVERT: E 146 GLU cc_start: 0.8627 (pp20) cc_final: 0.8220 (pp20) REVERT: E 149 ASP cc_start: 0.8709 (t0) cc_final: 0.7641 (p0) outliers start: 17 outliers final: 11 residues processed: 210 average time/residue: 0.5423 time to fit residues: 123.3392 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 : 0.418 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 210 VAL 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: 9.9990 chunk 68 optimal weight: 9.9990 chunk 104 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.064842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.052276 restraints weight = 30396.134| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 2.83 r_work: 0.2540 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11312 Z= 0.180 Angle : 0.674 10.307 15250 Z= 0.344 Chirality : 0.040 0.187 1705 Planarity : 0.004 0.042 1775 Dihedral : 14.017 170.300 2023 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.39 % Allowed : 22.41 % Favored : 76.20 % 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 aren not related in a simple way. whole: 3.81 (0.23), residues: 1305 helix: 3.09 (0.16), residues: 1015 sheet: None (None), residues: 0 loop : 0.35 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 179 TYR 0.009 0.001 TYR A 208 PHE 0.008 0.001 PHE B 199 TRP 0.010 0.001 TRP E 133 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00403 (11307) covalent geometry : angle 0.67398 (15250) hydrogen bonds : bond 0.05577 ( 846) hydrogen bonds : angle 3.99257 ( 2508) Misc. bond : bond 0.00040 ( 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 209 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9185 (mp0) cc_final: 0.8944 (mp0) REVERT: A 9 ASP cc_start: 0.8978 (m-30) cc_final: 0.8757 (m-30) REVERT: A 98 ASN cc_start: 0.9298 (t0) cc_final: 0.8952 (t0) REVERT: A 100 MET cc_start: 0.9462 (mmm) cc_final: 0.8888 (mmm) REVERT: A 149 ASP cc_start: 0.8661 (t0) cc_final: 0.8357 (t0) REVERT: A 174 LYS cc_start: 0.9322 (mmtt) cc_final: 0.9114 (mptp) REVERT: A 179 ARG cc_start: 0.9337 (ttp80) cc_final: 0.9022 (ttp-110) REVERT: B 98 ASN cc_start: 0.9299 (t0) cc_final: 0.8795 (t0) REVERT: B 149 ASP cc_start: 0.8989 (t0) cc_final: 0.8512 (t0) REVERT: B 214 MET cc_start: 0.8990 (mtp) cc_final: 0.8593 (ttm) REVERT: C 5 GLU cc_start: 0.9161 (mp0) cc_final: 0.8743 (mp0) REVERT: C 19 ASP cc_start: 0.9421 (t0) cc_final: 0.9043 (t70) REVERT: C 98 ASN cc_start: 0.9292 (t0) cc_final: 0.8766 (t0) REVERT: C 214 MET cc_start: 0.9083 (mtp) cc_final: 0.8694 (ttt) REVERT: C 233 SER cc_start: 0.9701 (m) cc_final: 0.9479 (p) REVERT: D 5 GLU cc_start: 0.9283 (mp0) cc_final: 0.9008 (mp0) REVERT: D 149 ASP cc_start: 0.8626 (t0) cc_final: 0.8204 (t0) REVERT: D 214 MET cc_start: 0.9109 (ttm) cc_final: 0.8844 (ttp) REVERT: E 5 GLU cc_start: 0.9170 (mp0) cc_final: 0.8742 (mp0) REVERT: E 98 ASN cc_start: 0.9262 (t0) cc_final: 0.8709 (t0) REVERT: E 100 MET cc_start: 0.9732 (mmm) cc_final: 0.9054 (mmm) REVERT: E 146 GLU cc_start: 0.8645 (pp20) cc_final: 0.8263 (pp20) REVERT: E 149 ASP cc_start: 0.8709 (t0) cc_final: 0.7657 (p0) REVERT: E 179 ARG cc_start: 0.9167 (ttp-110) cc_final: 0.8913 (ttp-110) outliers start: 15 outliers final: 13 residues processed: 201 average time/residue: 0.5512 time to fit residues: 119.9746 Evaluate side-chains 201 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 1 MET Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 39 VAL 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: 5.9990 chunk 122 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN E 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.067787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.055675 restraints weight = 29827.669| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.79 r_work: 0.2574 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11312 Z= 0.154 Angle : 0.676 10.901 15250 Z= 0.344 Chirality : 0.039 0.181 1705 Planarity : 0.004 0.037 1775 Dihedral : 13.801 169.919 2023 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.02 % Allowed : 23.06 % Favored : 75.93 % 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 aren not related in a simple way. whole: 3.79 (0.23), residues: 1305 helix: 3.09 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 0.31 (0.36), residues: 290 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 0.007 0.001 PHE E 199 TRP 0.013 0.001 TRP D 133 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00337 (11307) covalent geometry : angle 0.67640 (15250) hydrogen bonds : bond 0.05430 ( 846) hydrogen bonds : angle 3.95405 ( 2508) Misc. bond : bond 0.00013 ( 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 209 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9154 (mp0) cc_final: 0.8943 (mp0) REVERT: A 9 ASP cc_start: 0.8983 (m-30) cc_final: 0.8760 (m-30) REVERT: A 98 ASN cc_start: 0.9271 (t0) cc_final: 0.8724 (t0) REVERT: A 149 ASP cc_start: 0.8657 (t0) cc_final: 0.8355 (t0) REVERT: A 174 LYS cc_start: 0.9296 (mmtt) cc_final: 0.9082 (mptp) REVERT: A 179 ARG cc_start: 0.9330 (ttp80) cc_final: 0.9016 (ttp-110) REVERT: B 98 ASN cc_start: 0.9288 (t0) cc_final: 0.8759 (t0) REVERT: B 149 ASP cc_start: 0.8982 (t0) cc_final: 0.8519 (t0) REVERT: B 214 MET cc_start: 0.8939 (mtp) cc_final: 0.8539 (ttm) REVERT: C 5 GLU cc_start: 0.9144 (mp0) cc_final: 0.8740 (mp0) REVERT: C 19 ASP cc_start: 0.9422 (t0) cc_final: 0.9028 (t70) REVERT: C 98 ASN cc_start: 0.9278 (t0) cc_final: 0.8749 (t0) REVERT: C 214 MET cc_start: 0.9023 (mtp) cc_final: 0.8721 (ttm) REVERT: C 233 SER cc_start: 0.9699 (m) cc_final: 0.9478 (p) REVERT: D 5 GLU cc_start: 0.9292 (mp0) cc_final: 0.9031 (mp0) REVERT: D 120 GLU cc_start: 0.8810 (pm20) cc_final: 0.8599 (pm20) REVERT: D 149 ASP cc_start: 0.8608 (t0) cc_final: 0.8193 (t0) REVERT: E 5 GLU cc_start: 0.9140 (mp0) cc_final: 0.8739 (mp0) REVERT: E 98 ASN cc_start: 0.9222 (t0) cc_final: 0.8723 (t0) REVERT: E 100 MET cc_start: 0.9724 (mmm) cc_final: 0.9211 (mmm) REVERT: E 146 GLU cc_start: 0.8620 (pp20) cc_final: 0.8268 (pp20) REVERT: E 149 ASP cc_start: 0.8663 (t0) cc_final: 0.7625 (p0) REVERT: E 179 ARG cc_start: 0.9157 (ttp-110) cc_final: 0.8907 (ttp-110) outliers start: 11 outliers final: 11 residues processed: 203 average time/residue: 0.5750 time to fit residues: 126.5597 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 ------------------------------------------------------------------------------- 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 167 MET Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 39 VAL 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 96 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.064397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.051898 restraints weight = 30924.424| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 2.85 r_work: 0.2530 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11312 Z= 0.206 Angle : 0.695 11.066 15250 Z= 0.353 Chirality : 0.041 0.184 1705 Planarity : 0.004 0.034 1775 Dihedral : 13.690 169.715 2023 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.39 % Allowed : 22.69 % Favored : 75.93 % 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 aren not related in a simple way. whole: 3.78 (0.23), residues: 1305 helix: 3.09 (0.16), residues: 1015 sheet: None (None), residues: 0 loop : 0.29 (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 0.026 0.001 PHE D 199 TRP 0.010 0.001 TRP D 133 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00465 (11307) covalent geometry : angle 0.69491 (15250) hydrogen bonds : bond 0.05610 ( 846) hydrogen bonds : angle 4.03388 ( 2508) Misc. bond : bond 0.00055 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3655.72 seconds wall clock time: 63 minutes 11.74 seconds (3791.74 seconds total)