Starting phenix.real_space_refine on Sat Aug 23 09:06:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0m_18797/08_2025/8r0m_18797_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0m_18797/08_2025/8r0m_18797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r0m_18797/08_2025/8r0m_18797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0m_18797/08_2025/8r0m_18797.map" model { file = "/net/cci-nas-00/data/ceres_data/8r0m_18797/08_2025/8r0m_18797_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0m_18797/08_2025/8r0m_18797_neut.cif" } resolution = 2.87 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= 0.005 sd= 0.207 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 7421 2.51 5 N 1709 2.21 5 O 1930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11095 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2107 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2108 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2102 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2118 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2118 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 104 Unusual residues: {'LFA': 4, 'LMT': 1, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 99 Unusual residues: {'LFA': 4, 'LMT': 1, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 98 Unusual residues: {'LFA': 4, 'LMT': 1, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {'LFA': 4, 'LMT': 1, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 89 Unusual residues: {'LFA': 3, 'LMT': 1, 'RET': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 2.50, per 1000 atoms: 0.23 Number of scatterers: 11095 At special positions: 0 Unit cell: (94.024, 90.958, 82.782, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1930 8.00 N 1709 7.00 C 7421 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: 1.10 Conformation dependent library (CDL) restraints added in 405.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 10 sheets defined 78.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 14 through 42 Processing helix chain 'A' and resid 47 through 50 Processing helix chain 'A' and resid 51 through 77 Processing helix chain 'A' and resid 90 through 96 removed outlier: 3.863A pdb=" N ILE A 93 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 117 removed outlier: 4.044A pdb=" N VAL A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 3.949A pdb=" N VAL A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 148 Processing helix chain 'A' and resid 155 through 185 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 189 through 207 removed outlier: 3.585A pdb=" N LEU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.904A pdb=" N ALA A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 263 removed outlier: 3.805A pdb=" N PHE A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS A 249 " --> pdb=" O CYS A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 11 removed outlier: 3.985A pdb=" N ALA B 11 " --> pdb=" O PRO B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 42 Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 51 through 77 Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 97 through 117 removed outlier: 4.001A pdb=" N VAL B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Proline residue: B 108 - end of helix removed outlier: 3.946A pdb=" N VAL B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 148 removed outlier: 3.946A pdb=" N ARG B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 189 through 207 removed outlier: 3.581A pdb=" N LEU B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 3.905A pdb=" N ALA B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 Processing helix chain 'B' and resid 244 through 263 removed outlier: 3.678A pdb=" N HIS B 249 " --> pdb=" O CYS B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 42 Processing helix chain 'C' and resid 51 through 77 removed outlier: 3.703A pdb=" N ALA C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 97 through 117 removed outlier: 4.005A pdb=" N VAL C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Proline residue: C 108 - end of helix removed outlier: 3.954A pdb=" N VAL C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 148 removed outlier: 3.921A pdb=" N ARG C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 189 through 207 removed outlier: 3.585A pdb=" N LEU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.902A pdb=" N ALA C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 243 Processing helix chain 'C' and resid 244 through 263 removed outlier: 3.663A pdb=" N HIS C 249 " --> pdb=" O CYS C 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 11 removed outlier: 4.081A pdb=" N ALA D 11 " --> pdb=" O PRO D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 42 Processing helix chain 'D' and resid 47 through 50 Processing helix chain 'D' and resid 51 through 77 Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 97 through 117 removed outlier: 4.096A pdb=" N VAL D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Proline residue: D 108 - end of helix removed outlier: 3.931A pdb=" N VAL D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 148 Processing helix chain 'D' and resid 155 through 185 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 189 through 207 removed outlier: 3.592A pdb=" N LEU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 220 removed outlier: 3.936A pdb=" N ALA D 213 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR D 214 " --> pdb=" O TYR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 263 removed outlier: 3.838A pdb=" N PHE D 244 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 247 " --> pdb=" O GLY D 243 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS D 249 " --> pdb=" O CYS D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 42 Processing helix chain 'E' and resid 47 through 50 Processing helix chain 'E' and resid 51 through 77 Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'E' and resid 97 through 117 removed outlier: 3.999A pdb=" N VAL E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Proline residue: E 108 - end of helix removed outlier: 3.951A pdb=" N VAL E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 148 Processing helix chain 'E' and resid 155 through 185 Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 189 through 207 removed outlier: 3.585A pdb=" N LEU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 removed outlier: 3.902A pdb=" N ALA E 213 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 243 Processing helix chain 'E' and resid 244 through 263 removed outlier: 3.671A pdb=" N HIS E 249 " --> pdb=" O CYS E 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 82 Processing sheet with id=AA2, first strand: chain 'A' and resid 271 through 272 removed outlier: 6.474A pdb=" N ILE A 271 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 79 through 81 Processing sheet with id=AA4, first strand: chain 'B' and resid 271 through 272 removed outlier: 6.477A pdb=" N ILE B 271 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 81 Processing sheet with id=AA6, first strand: chain 'C' and resid 271 through 272 removed outlier: 6.474A pdb=" N ILE C 271 " --> pdb=" O GLN C 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.644A pdb=" N LEU D 85 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 271 through 272 removed outlier: 6.478A pdb=" N ILE D 271 " --> pdb=" O GLN D 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 79 through 81 Processing sheet with id=AB1, first strand: chain 'E' and resid 271 through 272 removed outlier: 6.446A pdb=" N ILE E 271 " --> pdb=" O GLN E 278 " (cutoff:3.500A) 846 hydrogen bonds defined for protein. 2484 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1572 1.30 - 1.43: 3027 1.43 - 1.56: 6617 1.56 - 1.69: 0 1.69 - 1.82: 60 Bond restraints: 11276 Sorted by residual: bond pdb=" C GLU E 17 " pdb=" O GLU E 17 " ideal model delta sigma weight residual 1.237 1.172 0.064 1.19e-02 7.06e+03 2.94e+01 bond pdb=" C GLY C 47 " pdb=" O GLY C 47 " ideal model delta sigma weight residual 1.232 1.183 0.049 9.40e-03 1.13e+04 2.68e+01 bond pdb=" C GLU D 17 " pdb=" O GLU D 17 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.26e-02 6.30e+03 2.18e+01 bond pdb=" CA SER E 275 " pdb=" CB SER E 275 " ideal model delta sigma weight residual 1.530 1.464 0.066 1.50e-02 4.44e+03 1.91e+01 bond pdb=" CA SER D 275 " pdb=" CB SER D 275 " ideal model delta sigma weight residual 1.530 1.467 0.062 1.50e-02 4.44e+03 1.72e+01 ... (remaining 11271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 12580 2.13 - 4.26: 2403 4.26 - 6.38: 294 6.38 - 8.51: 34 8.51 - 10.64: 11 Bond angle restraints: 15322 Sorted by residual: angle pdb=" C ALA A 106 " pdb=" N VAL A 107 " pdb=" CA VAL A 107 " ideal model delta sigma weight residual 120.24 114.85 5.39 6.30e-01 2.52e+00 7.32e+01 angle pdb=" C ALA E 106 " pdb=" N VAL E 107 " pdb=" CA VAL E 107 " ideal model delta sigma weight residual 120.24 114.87 5.37 6.30e-01 2.52e+00 7.27e+01 angle pdb=" C ALA C 106 " pdb=" N VAL C 107 " pdb=" CA VAL C 107 " ideal model delta sigma weight residual 120.24 114.87 5.37 6.30e-01 2.52e+00 7.26e+01 angle pdb=" C ALA B 106 " pdb=" N VAL B 107 " pdb=" CA VAL B 107 " ideal model delta sigma weight residual 120.24 114.88 5.36 6.30e-01 2.52e+00 7.25e+01 angle pdb=" C ALA D 106 " pdb=" N VAL D 107 " pdb=" CA VAL D 107 " ideal model delta sigma weight residual 120.24 114.96 5.28 6.30e-01 2.52e+00 7.02e+01 ... (remaining 15317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 6212 16.72 - 33.44: 371 33.44 - 50.16: 94 50.16 - 66.88: 18 66.88 - 83.60: 3 Dihedral angle restraints: 6698 sinusoidal: 2658 harmonic: 4040 Sorted by residual: dihedral pdb=" C ILE C 150 " pdb=" N ILE C 150 " pdb=" CA ILE C 150 " pdb=" CB ILE C 150 " ideal model delta harmonic sigma weight residual -122.00 -136.86 14.86 0 2.50e+00 1.60e-01 3.53e+01 dihedral pdb=" C ILE B 273 " pdb=" N ILE B 273 " pdb=" CA ILE B 273 " pdb=" CB ILE B 273 " ideal model delta harmonic sigma weight residual -122.00 -135.49 13.49 0 2.50e+00 1.60e-01 2.91e+01 dihedral pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CA ILE B 273 " pdb=" CB ILE B 273 " ideal model delta harmonic sigma weight residual 123.40 135.64 -12.24 0 2.50e+00 1.60e-01 2.40e+01 ... (remaining 6695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1514 0.096 - 0.193: 349 0.193 - 0.289: 35 0.289 - 0.386: 0 0.386 - 0.482: 2 Chirality restraints: 1900 Sorted by residual: chirality pdb=" CA ILE B 273 " pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CB ILE B 273 " both_signs ideal model delta sigma weight residual False 2.43 1.95 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CA ILE C 150 " pdb=" N ILE C 150 " pdb=" C ILE C 150 " pdb=" CB ILE C 150 " both_signs ideal model delta sigma weight residual False 2.43 1.96 0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CA VAL C 82 " pdb=" N VAL C 82 " pdb=" C VAL C 82 " pdb=" CB VAL C 82 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1897 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 49 " 0.568 9.50e-02 1.11e+02 2.55e-01 3.96e+01 pdb=" NE ARG C 49 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG C 49 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 49 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 49 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 50 " -0.048 2.00e-02 2.50e+03 3.07e-02 1.88e+01 pdb=" CG TYR E 50 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR E 50 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR E 50 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR E 50 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR E 50 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR E 50 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 50 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 126 " -0.366 9.50e-02 1.11e+02 1.65e-01 1.86e+01 pdb=" NE ARG E 126 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG E 126 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG E 126 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG E 126 " -0.005 2.00e-02 2.50e+03 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 807 2.70 - 3.25: 11090 3.25 - 3.80: 18645 3.80 - 4.35: 26171 4.35 - 4.90: 42185 Nonbonded interactions: 98898 Sorted by model distance: nonbonded pdb=" OH TYR D 79 " pdb=" O HOH D 501 " model vdw 2.147 3.040 nonbonded pdb=" OH TYR A 79 " pdb=" O HOH A 501 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR E 79 " pdb=" O HOH E 501 " model vdw 2.157 3.040 nonbonded pdb=" OH TYR B 79 " pdb=" O HOH B 501 " model vdw 2.160 3.040 nonbonded pdb=" OD2 ASP C 80 " pdb=" ND2 ASN C 89 " model vdw 2.221 3.120 ... (remaining 98893 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 3 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 through 128 or (resid 129 and (name N or \ name CA or name C or name O or name CB or name CG or name CD )) or resid 130 th \ rough 190 or (resid 191 through 194 and (name N or name CA or name C or name O o \ r name CB )) or resid 195 through 402 or (resid 403 and (name C7 )) or (resid 40 \ 4 and (name C13 or name C14 or name C15 or name C16)))) selection = (chain 'B' and (resid 3 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or (resid 127 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD )) or resid 128 through 181 or (resid 182 a \ nd (name N or name CA or name C or name O or name CB )) or resid 183 through 401 \ or (resid 402 and (name C1 or name C10 or name C11 or name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 403 and \ (name C7 )) or (resid 404 and (name C13 or name C14 or name C15 or name C16)))) \ selection = (chain 'C' and (resid 3 through 181 or (resid 182 and (name N or name CA or name \ C or name O or name CB )) or resid 183 through 401 or (resid 402 and (name C1 o \ r name C10 or name C11 or name C2 or name C3 or name C4 or name C5 or name C6 or \ name C7 or name C8 or name C9 )) or (resid 403 and (name C7 )) or (resid 404 an \ d (name C12 or name C13 or name C14 or name C15)))) selection = (chain 'D' and (resid 3 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 through 151 or (resid 152 and (name N or \ name CA or name C or name O or name CB )) or resid 153 through 181 or (resid 18 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 183 through \ 190 or (resid 191 through 194 and (name N or name CA or name C or name O or name \ CB )) or resid 195 through 249 or (resid 250 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name NE )) or resid 251 through 401 \ or (resid 402 and (name C1 or name C10 or name C11 or name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 403 and \ (name C7 )) or (resid 404 and (name C13 or name C14 or name C15 or name C16)))) \ selection = (chain 'E' and (resid 3 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or (resid 127 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD )) or resid 128 through 151 or (resid 152 a \ nd (name N or name CA or name C or name O or name CB )) or resid 153 or (resid 1 \ 54 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name NE )) or resid 155 through 181 or (resid 182 and (name N or name CA or na \ me C or name O or name CB )) or resid 183 through 190 or (resid 191 through 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 40 \ 1 or (resid 402 and (name C1 or name C10 or name C11 or name C2 or name C3 or na \ me C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 403 an \ d (name C7 )) or (resid 404 and (name C13 or name C14 or name C15 or name C16))) \ ) } 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 10.650 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 : 0.013 0.090 11281 Z= 0.852 Angle : 1.687 10.638 15322 Z= 1.159 Chirality : 0.079 0.482 1900 Planarity : 0.016 0.255 1770 Dihedral : 12.083 83.598 4098 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.44 % Allowed : 2.72 % Favored : 94.84 % Cbeta Deviations : 0.62 % 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: -4.05 (0.16), residues: 1400 helix: -2.60 (0.11), residues: 990 sheet: None (None), residues: 0 loop : -2.34 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.004 ARG E 126 TYR 0.051 0.012 TYR E 50 PHE 0.034 0.009 PHE E 141 TRP 0.042 0.009 TRP B 272 HIS 0.012 0.004 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.01264 (11276) covalent geometry : angle 1.68707 (15322) hydrogen bonds : bond 0.23678 ( 846) hydrogen bonds : angle 9.06428 ( 2484) Misc. bond : bond 0.02664 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.401 Fit side-chains REVERT: A 43 ARG cc_start: 0.8483 (ptt-90) cc_final: 0.8255 (ptt90) REVERT: A 82 VAL cc_start: 0.7863 (t) cc_final: 0.7599 (m) REVERT: A 191 GLU cc_start: 0.8378 (tt0) cc_final: 0.7316 (mp0) REVERT: A 247 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8327 (tt) REVERT: A 259 ASP cc_start: 0.8605 (m-30) cc_final: 0.8373 (m-30) REVERT: A 280 ASP cc_start: 0.8762 (m-30) cc_final: 0.8560 (m-30) REVERT: B 82 VAL cc_start: 0.8212 (t) cc_final: 0.7998 (m) REVERT: B 259 ASP cc_start: 0.8574 (m-30) cc_final: 0.8340 (m-30) REVERT: C 82 VAL cc_start: 0.8458 (t) cc_final: 0.8235 (m) REVERT: C 259 ASP cc_start: 0.8579 (m-30) cc_final: 0.8349 (m-30) REVERT: D 259 ASP cc_start: 0.8408 (m-30) cc_final: 0.8167 (m-30) REVERT: E 43 ARG cc_start: 0.8587 (ptt-90) cc_final: 0.8358 (ptt90) REVERT: E 126 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.6305 (mmt90) REVERT: E 247 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8174 (tt) outliers start: 26 outliers final: 7 residues processed: 165 average time/residue: 0.4869 time to fit residues: 87.0065 Evaluate side-chains 131 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 126 ARG Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN B 15 GLN B 230 HIS C 187 GLN C 230 HIS D 15 GLN D 230 HIS E 18 HIS E 230 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.104692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.092074 restraints weight = 12331.288| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.14 r_work: 0.2876 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11281 Z= 0.138 Angle : 0.567 5.457 15322 Z= 0.305 Chirality : 0.040 0.130 1900 Planarity : 0.005 0.034 1770 Dihedral : 9.614 59.487 2014 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.54 % Allowed : 5.26 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.90 (0.21), residues: 1400 helix: 1.31 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -1.34 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 126 TYR 0.012 0.002 TYR A 68 PHE 0.013 0.002 PHE C 24 TRP 0.014 0.001 TRP C 162 HIS 0.007 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00295 (11276) covalent geometry : angle 0.56739 (15322) hydrogen bonds : bond 0.05212 ( 846) hydrogen bonds : angle 3.85019 ( 2484) Misc. bond : bond 0.00025 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.404 Fit side-chains REVERT: A 191 GLU cc_start: 0.8153 (tt0) cc_final: 0.7349 (mp0) REVERT: A 204 MET cc_start: 0.9056 (mmp) cc_final: 0.8802 (mmp) REVERT: A 247 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8035 (mt) REVERT: A 280 ASP cc_start: 0.8402 (m-30) cc_final: 0.8140 (m-30) REVERT: B 82 VAL cc_start: 0.8336 (t) cc_final: 0.8132 (m) REVERT: C 172 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.8015 (mt) REVERT: C 259 ASP cc_start: 0.8108 (m-30) cc_final: 0.7905 (m-30) REVERT: D 259 ASP cc_start: 0.8163 (m-30) cc_final: 0.7931 (m-30) REVERT: D 271 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8455 (mp) REVERT: E 49 ARG cc_start: 0.8777 (ttt180) cc_final: 0.8535 (ttt180) REVERT: E 126 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6340 (mmt90) outliers start: 27 outliers final: 9 residues processed: 147 average time/residue: 0.4473 time to fit residues: 71.9740 Evaluate side-chains 124 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 126 ARG Chi-restraints excluded: chain E residue 268 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 58 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.102669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.090378 restraints weight = 12587.030| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.10 r_work: 0.2852 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11281 Z= 0.157 Angle : 0.546 5.617 15322 Z= 0.288 Chirality : 0.041 0.134 1900 Planarity : 0.005 0.035 1770 Dihedral : 9.268 59.837 2004 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.10 % Allowed : 6.38 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.22), residues: 1400 helix: 2.64 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -1.07 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 126 TYR 0.015 0.002 TYR A 68 PHE 0.013 0.002 PHE E 34 TRP 0.013 0.001 TRP C 162 HIS 0.005 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00370 (11276) covalent geometry : angle 0.54632 (15322) hydrogen bonds : bond 0.04952 ( 846) hydrogen bonds : angle 3.56928 ( 2484) Misc. bond : bond 0.00038 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.401 Fit side-chains REVERT: A 191 GLU cc_start: 0.8177 (tt0) cc_final: 0.7301 (mp0) REVERT: A 280 ASP cc_start: 0.8467 (m-30) cc_final: 0.8216 (m-30) REVERT: C 130 LEU cc_start: 0.7516 (tp) cc_final: 0.7309 (mt) REVERT: C 271 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8606 (mp) REVERT: D 40 TRP cc_start: 0.8011 (t-100) cc_final: 0.7802 (t-100) REVERT: D 259 ASP cc_start: 0.8198 (m-30) cc_final: 0.7992 (m-30) REVERT: E 49 ARG cc_start: 0.8808 (ttt180) cc_final: 0.8584 (ttt180) REVERT: E 126 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.6224 (mmt90) REVERT: E 269 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8001 (pt0) outliers start: 33 outliers final: 15 residues processed: 140 average time/residue: 0.4626 time to fit residues: 70.6417 Evaluate side-chains 128 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 126 ARG Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 82 optimal weight: 0.2980 chunk 101 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.105283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.092738 restraints weight = 12595.573| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.16 r_work: 0.2894 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11281 Z= 0.118 Angle : 0.481 4.955 15322 Z= 0.254 Chirality : 0.039 0.135 1900 Planarity : 0.004 0.036 1770 Dihedral : 8.396 58.265 2002 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.54 % Allowed : 8.26 % Favored : 89.20 % 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: 3.33 (0.22), residues: 1400 helix: 3.24 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.91 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 126 TYR 0.012 0.002 TYR A 68 PHE 0.010 0.001 PHE C 24 TRP 0.011 0.001 TRP C 162 HIS 0.005 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00255 (11276) covalent geometry : angle 0.48102 (15322) hydrogen bonds : bond 0.04167 ( 846) hydrogen bonds : angle 3.33082 ( 2484) Misc. bond : bond 0.00015 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.328 Fit side-chains REVERT: A 280 ASP cc_start: 0.8406 (m-30) cc_final: 0.8156 (m-30) REVERT: B 66 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7683 (mm) REVERT: C 271 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8577 (mp) REVERT: D 40 TRP cc_start: 0.8014 (t-100) cc_final: 0.7767 (t-100) REVERT: D 247 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7679 (mt) REVERT: D 269 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7618 (pt0) REVERT: E 49 ARG cc_start: 0.8802 (ttt180) cc_final: 0.8590 (ttt180) REVERT: E 126 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.6209 (mmt90) REVERT: E 268 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8492 (p) REVERT: E 269 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7979 (pt0) outliers start: 27 outliers final: 12 residues processed: 153 average time/residue: 0.4391 time to fit residues: 73.4014 Evaluate side-chains 139 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 126 ARG Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.103657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.091240 restraints weight = 12596.097| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.12 r_work: 0.2857 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11281 Z= 0.140 Angle : 0.501 4.868 15322 Z= 0.263 Chirality : 0.041 0.141 1900 Planarity : 0.004 0.036 1770 Dihedral : 8.373 59.034 2002 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.54 % Allowed : 9.58 % Favored : 87.89 % 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: 3.42 (0.22), residues: 1400 helix: 3.29 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.81 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 126 TYR 0.013 0.002 TYR A 68 PHE 0.011 0.001 PHE C 137 TRP 0.011 0.001 TRP C 162 HIS 0.005 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00324 (11276) covalent geometry : angle 0.50106 (15322) hydrogen bonds : bond 0.04440 ( 846) hydrogen bonds : angle 3.34474 ( 2484) Misc. bond : bond 0.00037 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.341 Fit side-chains REVERT: A 271 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8491 (mp) REVERT: A 280 ASP cc_start: 0.8414 (m-30) cc_final: 0.8153 (m-30) REVERT: C 271 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8564 (mp) REVERT: D 40 TRP cc_start: 0.8056 (t-100) cc_final: 0.7829 (t-100) REVERT: D 247 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7773 (mt) REVERT: D 269 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: E 49 ARG cc_start: 0.8832 (ttt180) cc_final: 0.8593 (ttt180) REVERT: E 268 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8481 (p) REVERT: E 269 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8014 (pt0) outliers start: 27 outliers final: 15 residues processed: 139 average time/residue: 0.4106 time to fit residues: 62.7590 Evaluate side-chains 134 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 68 optimal weight: 0.8980 chunk 138 optimal weight: 0.0470 chunk 49 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.102067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.089574 restraints weight = 12775.546| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.11 r_work: 0.2841 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11281 Z= 0.161 Angle : 0.520 5.142 15322 Z= 0.272 Chirality : 0.042 0.166 1900 Planarity : 0.004 0.037 1770 Dihedral : 8.469 59.293 1997 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.91 % Allowed : 9.48 % Favored : 87.61 % 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: 3.39 (0.22), residues: 1400 helix: 3.26 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.79 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 126 TYR 0.015 0.002 TYR A 68 PHE 0.016 0.002 PHE E 202 TRP 0.011 0.001 TRP C 162 HIS 0.005 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00385 (11276) covalent geometry : angle 0.52000 (15322) hydrogen bonds : bond 0.04725 ( 846) hydrogen bonds : angle 3.39357 ( 2484) Misc. bond : bond 0.00055 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.415 Fit side-chains REVERT: A 191 GLU cc_start: 0.8187 (tt0) cc_final: 0.7366 (mp0) REVERT: A 271 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8526 (mp) REVERT: A 280 ASP cc_start: 0.8465 (m-30) cc_final: 0.8194 (m-30) REVERT: C 271 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8635 (mp) REVERT: D 40 TRP cc_start: 0.8068 (t-100) cc_final: 0.7860 (t-100) REVERT: E 49 ARG cc_start: 0.8840 (ttt180) cc_final: 0.8601 (ttt180) REVERT: E 268 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8518 (p) REVERT: E 269 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8088 (pt0) outliers start: 31 outliers final: 15 residues processed: 131 average time/residue: 0.4150 time to fit residues: 59.5353 Evaluate side-chains 129 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 137 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.104901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.092495 restraints weight = 12488.327| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.11 r_work: 0.2884 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11281 Z= 0.121 Angle : 0.475 4.824 15322 Z= 0.249 Chirality : 0.040 0.151 1900 Planarity : 0.004 0.037 1770 Dihedral : 8.011 59.020 1997 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.35 % Allowed : 9.86 % Favored : 87.79 % 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: 3.71 (0.22), residues: 1400 helix: 3.49 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.66 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 126 TYR 0.012 0.002 TYR A 68 PHE 0.014 0.001 PHE E 202 TRP 0.011 0.001 TRP C 162 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00271 (11276) covalent geometry : angle 0.47462 (15322) hydrogen bonds : bond 0.04130 ( 846) hydrogen bonds : angle 3.26838 ( 2484) Misc. bond : bond 0.00025 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.415 Fit side-chains REVERT: A 271 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8455 (mp) REVERT: A 280 ASP cc_start: 0.8409 (m-30) cc_final: 0.8132 (m-30) REVERT: C 271 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8576 (mp) REVERT: D 40 TRP cc_start: 0.8099 (t-100) cc_final: 0.7866 (t-100) REVERT: D 139 MET cc_start: 0.8686 (ttp) cc_final: 0.8372 (ttp) REVERT: E 49 ARG cc_start: 0.8817 (ttt180) cc_final: 0.8573 (ttt180) REVERT: E 268 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8460 (p) REVERT: E 269 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8086 (pt0) outliers start: 25 outliers final: 18 residues processed: 141 average time/residue: 0.4645 time to fit residues: 71.7385 Evaluate side-chains 142 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 107 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN C 81 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.102954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.092388 restraints weight = 12490.543| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 0.83 r_work: 0.2850 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11281 Z= 0.222 Angle : 0.580 5.180 15322 Z= 0.302 Chirality : 0.044 0.145 1900 Planarity : 0.005 0.038 1770 Dihedral : 8.798 57.796 1997 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.82 % Allowed : 10.23 % Favored : 86.95 % 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: 3.13 (0.22), residues: 1400 helix: 3.06 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.86 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 51 TYR 0.017 0.003 TYR A 68 PHE 0.025 0.002 PHE E 202 TRP 0.010 0.001 TRP C 162 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00549 (11276) covalent geometry : angle 0.57954 (15322) hydrogen bonds : bond 0.05341 ( 846) hydrogen bonds : angle 3.52914 ( 2484) Misc. bond : bond 0.00097 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.262 Fit side-chains REVERT: A 191 GLU cc_start: 0.8330 (tt0) cc_final: 0.7652 (mp0) REVERT: A 271 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8515 (mp) REVERT: A 280 ASP cc_start: 0.8606 (m-30) cc_final: 0.8324 (m-30) REVERT: C 271 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8675 (mp) REVERT: C 283 ILE cc_start: 0.8130 (pt) cc_final: 0.7785 (pt) REVERT: E 49 ARG cc_start: 0.8862 (ttt180) cc_final: 0.8622 (ttt180) REVERT: E 269 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8175 (pt0) outliers start: 30 outliers final: 20 residues processed: 129 average time/residue: 0.4244 time to fit residues: 60.1424 Evaluate side-chains 134 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.101300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.090447 restraints weight = 12460.996| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 0.85 r_work: 0.2877 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11281 Z= 0.168 Angle : 0.529 4.911 15322 Z= 0.277 Chirality : 0.042 0.143 1900 Planarity : 0.004 0.038 1770 Dihedral : 8.599 59.262 1997 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.54 % Allowed : 10.52 % Favored : 86.95 % 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: 3.28 (0.22), residues: 1400 helix: 3.19 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.85 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 126 TYR 0.014 0.002 TYR A 68 PHE 0.024 0.002 PHE E 202 TRP 0.011 0.001 TRP C 162 HIS 0.005 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00405 (11276) covalent geometry : angle 0.52854 (15322) hydrogen bonds : bond 0.04768 ( 846) hydrogen bonds : angle 3.42498 ( 2484) Misc. bond : bond 0.00061 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.394 Fit side-chains REVERT: A 191 GLU cc_start: 0.8306 (tt0) cc_final: 0.7635 (mp0) REVERT: A 271 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8531 (mp) REVERT: A 280 ASP cc_start: 0.8587 (m-30) cc_final: 0.8301 (m-30) REVERT: C 271 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8657 (mp) REVERT: C 283 ILE cc_start: 0.8096 (pt) cc_final: 0.7748 (pt) REVERT: E 49 ARG cc_start: 0.8841 (ttt180) cc_final: 0.8592 (ttt180) REVERT: E 62 ILE cc_start: 0.8485 (mt) cc_final: 0.8190 (tt) REVERT: E 268 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8483 (p) REVERT: E 269 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8093 (pt0) outliers start: 27 outliers final: 19 residues processed: 130 average time/residue: 0.4251 time to fit residues: 60.2565 Evaluate side-chains 134 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.104617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.091972 restraints weight = 12556.408| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.14 r_work: 0.2875 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11281 Z= 0.126 Angle : 0.483 4.770 15322 Z= 0.254 Chirality : 0.041 0.170 1900 Planarity : 0.004 0.038 1770 Dihedral : 8.128 59.626 1997 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.25 % Allowed : 10.89 % Favored : 86.85 % 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: 3.63 (0.22), residues: 1400 helix: 3.45 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.76 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 126 TYR 0.012 0.002 TYR A 68 PHE 0.023 0.001 PHE E 202 TRP 0.011 0.001 TRP C 162 HIS 0.005 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00284 (11276) covalent geometry : angle 0.48308 (15322) hydrogen bonds : bond 0.04189 ( 846) hydrogen bonds : angle 3.29066 ( 2484) Misc. bond : bond 0.00031 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.283 Fit side-chains REVERT: A 271 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8458 (mp) REVERT: A 280 ASP cc_start: 0.8446 (m-30) cc_final: 0.8153 (m-30) REVERT: C 271 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8623 (mp) REVERT: C 283 ILE cc_start: 0.8044 (pt) cc_final: 0.7692 (pt) REVERT: E 49 ARG cc_start: 0.8847 (ttt180) cc_final: 0.8605 (ttt180) REVERT: E 62 ILE cc_start: 0.8462 (mt) cc_final: 0.8170 (tt) REVERT: E 268 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8468 (p) REVERT: E 269 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8125 (pt0) outliers start: 24 outliers final: 19 residues processed: 134 average time/residue: 0.4047 time to fit residues: 59.6460 Evaluate side-chains 139 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 43 optimal weight: 0.0270 chunk 23 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.106930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.094121 restraints weight = 12449.919| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.17 r_work: 0.2897 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11281 Z= 0.108 Angle : 0.461 4.839 15322 Z= 0.241 Chirality : 0.040 0.202 1900 Planarity : 0.004 0.038 1770 Dihedral : 7.681 59.899 1997 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.88 % Allowed : 11.36 % Favored : 86.76 % 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: 3.90 (0.22), residues: 1400 helix: 3.69 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -0.72 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 126 TYR 0.012 0.001 TYR B 68 PHE 0.024 0.001 PHE E 202 TRP 0.011 0.001 TRP C 162 HIS 0.005 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00232 (11276) covalent geometry : angle 0.46102 (15322) hydrogen bonds : bond 0.03816 ( 846) hydrogen bonds : angle 3.19321 ( 2484) Misc. bond : bond 0.00016 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.25 seconds wall clock time: 44 minutes 17.14 seconds (2657.14 seconds total)