Starting phenix.real_space_refine on Fri Mar 6 13:16:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xni_33316/03_2026/7xni_33316_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xni_33316/03_2026/7xni_33316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xni_33316/03_2026/7xni_33316_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xni_33316/03_2026/7xni_33316_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xni_33316/03_2026/7xni_33316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xni_33316/03_2026/7xni_33316.map" } resolution = 3.5 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= -0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 80 5.16 5 C 10132 2.51 5 N 2688 2.21 5 O 2816 1.98 5 H 15652 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31368 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "B" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "C" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "E" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "H" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 5.02, per 1000 atoms: 0.16 Number of scatterers: 31368 At special positions: 0 Unit cell: (114.582, 114.582, 123.708, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 O 2816 8.00 N 2688 7.00 C 10132 6.00 H 15652 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 808.1 milliseconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 4 sheets defined 79.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 119 through 143 removed outlier: 3.593A pdb=" N PHE A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 178 removed outlier: 4.119A pdb=" N PHE A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 186 through 194 Processing helix chain 'A' and resid 196 through 216 Processing helix chain 'A' and resid 224 through 237 removed outlier: 3.982A pdb=" N PHE A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 4.442A pdb=" N ASP A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 258 through 285 Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.664A pdb=" N THR A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 362 removed outlier: 4.780A pdb=" N SER A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.660A pdb=" N ALA A 370 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.962A pdb=" N TRP A 392 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 533 removed outlier: 3.917A pdb=" N THR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 564 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 119 through 143 removed outlier: 3.594A pdb=" N PHE B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 178 removed outlier: 4.118A pdb=" N PHE B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 161 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 186 through 194 Processing helix chain 'B' and resid 196 through 216 Processing helix chain 'B' and resid 224 through 237 removed outlier: 3.982A pdb=" N PHE B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 removed outlier: 4.442A pdb=" N ASP B 242 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 258 through 285 Processing helix chain 'B' and resid 298 through 311 removed outlier: 3.663A pdb=" N THR B 311 " --> pdb=" O VAL B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 362 removed outlier: 4.780A pdb=" N SER B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 366 through 385 removed outlier: 3.660A pdb=" N ALA B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 385 " --> pdb=" O CYS B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 removed outlier: 3.964A pdb=" N TRP B 392 " --> pdb=" O SER B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 533 removed outlier: 3.917A pdb=" N THR B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 564 Processing helix chain 'C' and resid 7 through 22 Processing helix chain 'C' and resid 29 through 40 removed outlier: 4.200A pdb=" N VAL C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 65 through 75 Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.695A pdb=" N GLU C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 118 through 128 removed outlier: 3.645A pdb=" N ARG C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'D' and resid 105 through 116 Processing helix chain 'D' and resid 119 through 143 removed outlier: 3.593A pdb=" N PHE D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 178 removed outlier: 4.119A pdb=" N PHE D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE D 161 " --> pdb=" O PHE D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 186 through 194 Processing helix chain 'D' and resid 196 through 216 Processing helix chain 'D' and resid 224 through 237 removed outlier: 3.982A pdb=" N PHE D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 242 removed outlier: 4.442A pdb=" N ASP D 242 " --> pdb=" O LEU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 258 Processing helix chain 'D' and resid 258 through 285 Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.663A pdb=" N THR D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 362 removed outlier: 4.780A pdb=" N SER D 338 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 366 through 385 removed outlier: 3.661A pdb=" N ALA D 370 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 385 " --> pdb=" O CYS D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 395 removed outlier: 3.963A pdb=" N TRP D 392 " --> pdb=" O SER D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 533 removed outlier: 3.917A pdb=" N THR D 513 " --> pdb=" O HIS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 564 Processing helix chain 'E' and resid 7 through 22 Processing helix chain 'E' and resid 29 through 40 removed outlier: 4.201A pdb=" N VAL E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 65 through 75 Processing helix chain 'E' and resid 79 through 91 removed outlier: 3.696A pdb=" N GLU E 83 " --> pdb=" O ASP E 79 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG E 91 " --> pdb=" O ARG E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 118 through 128 removed outlier: 3.645A pdb=" N ARG E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'F' and resid 7 through 22 Processing helix chain 'F' and resid 29 through 40 removed outlier: 4.201A pdb=" N VAL F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 54 Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 79 through 91 removed outlier: 3.696A pdb=" N GLU F 83 " --> pdb=" O ASP F 79 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG F 91 " --> pdb=" O ARG F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 118 through 128 removed outlier: 3.645A pdb=" N ARG F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'G' and resid 105 through 116 Processing helix chain 'G' and resid 119 through 143 removed outlier: 3.593A pdb=" N PHE G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 178 removed outlier: 4.118A pdb=" N PHE G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE G 161 " --> pdb=" O PHE G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 186 through 194 Processing helix chain 'G' and resid 196 through 216 Processing helix chain 'G' and resid 224 through 237 removed outlier: 3.982A pdb=" N PHE G 232 " --> pdb=" O ARG G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 242 removed outlier: 4.443A pdb=" N ASP G 242 " --> pdb=" O LEU G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 258 Processing helix chain 'G' and resid 258 through 285 Processing helix chain 'G' and resid 298 through 311 removed outlier: 3.663A pdb=" N THR G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 362 removed outlier: 4.781A pdb=" N SER G 338 " --> pdb=" O VAL G 334 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE G 339 " --> pdb=" O PHE G 335 " (cutoff:3.500A) Proline residue: G 343 - end of helix Processing helix chain 'G' and resid 366 through 385 removed outlier: 3.660A pdb=" N ALA G 370 " --> pdb=" O ARG G 366 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU G 385 " --> pdb=" O CYS G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 395 removed outlier: 3.963A pdb=" N TRP G 392 " --> pdb=" O SER G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 509 through 533 removed outlier: 3.917A pdb=" N THR G 513 " --> pdb=" O HIS G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 564 Processing helix chain 'H' and resid 7 through 22 Processing helix chain 'H' and resid 29 through 40 removed outlier: 4.201A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 54 Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 79 through 91 removed outlier: 3.695A pdb=" N GLU H 83 " --> pdb=" O ASP H 79 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU H 84 " --> pdb=" O THR H 80 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 94 No H-bonds generated for 'chain 'H' and resid 92 through 94' Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 118 through 128 removed outlier: 3.646A pdb=" N ARG H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 147 Processing sheet with id=AA1, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 1097 hydrogen bonds defined for protein. 3243 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: 6.85 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15628 1.03 - 1.22: 44 1.22 - 1.42: 6863 1.42 - 1.62: 9025 1.62 - 1.81: 136 Bond restraints: 31696 Sorted by residual: bond pdb=" NE ARG A 192 " pdb=" HE ARG A 192 " ideal model delta sigma weight residual 0.860 0.971 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" NE ARG G 192 " pdb=" HE ARG G 192 " ideal model delta sigma weight residual 0.860 0.971 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" NE ARG A 109 " pdb=" HE ARG A 109 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" NE ARG B 109 " pdb=" HE ARG B 109 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG D 109 " pdb=" HE ARG D 109 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 31691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 55312 2.48 - 4.96: 1515 4.96 - 7.44: 215 7.44 - 9.92: 22 9.92 - 12.39: 8 Bond angle restraints: 57072 Sorted by residual: angle pdb=" CB ARG G 190 " pdb=" CG ARG G 190 " pdb=" CD ARG G 190 " ideal model delta sigma weight residual 111.30 123.69 -12.39 2.30e+00 1.89e-01 2.90e+01 angle pdb=" CB ARG B 190 " pdb=" CG ARG B 190 " pdb=" CD ARG B 190 " ideal model delta sigma weight residual 111.30 123.69 -12.39 2.30e+00 1.89e-01 2.90e+01 angle pdb=" CB ARG A 190 " pdb=" CG ARG A 190 " pdb=" CD ARG A 190 " ideal model delta sigma weight residual 111.30 123.68 -12.38 2.30e+00 1.89e-01 2.90e+01 angle pdb=" CB ARG D 190 " pdb=" CG ARG D 190 " pdb=" CD ARG D 190 " ideal model delta sigma weight residual 111.30 123.68 -12.38 2.30e+00 1.89e-01 2.90e+01 angle pdb=" CG ARG D 190 " pdb=" CD ARG D 190 " pdb=" NE ARG D 190 " ideal model delta sigma weight residual 112.00 101.73 10.27 2.20e+00 2.07e-01 2.18e+01 ... (remaining 57067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 13274 14.98 - 29.96: 1062 29.96 - 44.94: 264 44.94 - 59.92: 157 59.92 - 74.90: 23 Dihedral angle restraints: 14780 sinusoidal: 7864 harmonic: 6916 Sorted by residual: dihedral pdb=" CA ARG C 75 " pdb=" C ARG C 75 " pdb=" N LYS C 76 " pdb=" CA LYS C 76 " ideal model delta harmonic sigma weight residual -180.00 -155.80 -24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ARG H 75 " pdb=" C ARG H 75 " pdb=" N LYS H 76 " pdb=" CA LYS H 76 " ideal model delta harmonic sigma weight residual 180.00 -155.81 -24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ARG E 75 " pdb=" C ARG E 75 " pdb=" N LYS E 76 " pdb=" CA LYS E 76 " ideal model delta harmonic sigma weight residual -180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 14777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1748 0.067 - 0.134: 533 0.134 - 0.201: 109 0.201 - 0.268: 30 0.268 - 0.335: 8 Chirality restraints: 2428 Sorted by residual: chirality pdb=" CA LYS A 121 " pdb=" N LYS A 121 " pdb=" C LYS A 121 " pdb=" CB LYS A 121 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA LYS B 121 " pdb=" N LYS B 121 " pdb=" C LYS B 121 " pdb=" CB LYS B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA LYS G 121 " pdb=" N LYS G 121 " pdb=" C LYS G 121 " pdb=" CB LYS G 121 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 2425 not shown) Planarity restraints: 4648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 184 " -0.028 2.00e-02 2.50e+03 3.14e-02 2.96e+01 pdb=" CG TYR B 184 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 184 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR B 184 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR B 184 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR B 184 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 184 " 0.062 2.00e-02 2.50e+03 pdb=" OH TYR B 184 " -0.034 2.00e-02 2.50e+03 pdb=" HD1 TYR B 184 " 0.023 2.00e-02 2.50e+03 pdb=" HD2 TYR B 184 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TYR B 184 " -0.012 2.00e-02 2.50e+03 pdb=" HE2 TYR B 184 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 184 " -0.028 2.00e-02 2.50e+03 3.13e-02 2.93e+01 pdb=" CG TYR G 184 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR G 184 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR G 184 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR G 184 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR G 184 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR G 184 " 0.062 2.00e-02 2.50e+03 pdb=" OH TYR G 184 " -0.034 2.00e-02 2.50e+03 pdb=" HD1 TYR G 184 " 0.022 2.00e-02 2.50e+03 pdb=" HD2 TYR G 184 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TYR G 184 " -0.012 2.00e-02 2.50e+03 pdb=" HE2 TYR G 184 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 184 " -0.028 2.00e-02 2.50e+03 3.12e-02 2.92e+01 pdb=" CG TYR A 184 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 184 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 184 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 184 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 184 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 184 " 0.062 2.00e-02 2.50e+03 pdb=" OH TYR A 184 " -0.034 2.00e-02 2.50e+03 pdb=" HD1 TYR A 184 " 0.023 2.00e-02 2.50e+03 pdb=" HD2 TYR A 184 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TYR A 184 " -0.012 2.00e-02 2.50e+03 pdb=" HE2 TYR A 184 " 0.012 2.00e-02 2.50e+03 ... (remaining 4645 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1614 2.15 - 2.76: 62968 2.76 - 3.37: 86678 3.37 - 3.99: 105816 3.99 - 4.60: 168342 Nonbonded interactions: 425418 Sorted by model distance: nonbonded pdb=" H ASN G 289 " pdb=" O ARG G 293 " model vdw 1.536 2.450 nonbonded pdb=" H ASN B 289 " pdb=" O ARG B 293 " model vdw 1.537 2.450 nonbonded pdb=" H ASN A 289 " pdb=" O ARG A 293 " model vdw 1.537 2.450 nonbonded pdb=" H ASN D 289 " pdb=" O ARG D 293 " model vdw 1.537 2.450 nonbonded pdb=" O ARG D 360 " pdb=" HD1 HIS D 363 " model vdw 1.595 2.450 ... (remaining 425413 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' } 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 group one per residue 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: 0.950 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: 0.160 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.730 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 0.012 0.102 16044 Z= 0.539 Angle : 1.226 12.395 21680 Z= 0.720 Chirality : 0.070 0.335 2428 Planarity : 0.007 0.042 2732 Dihedral : 11.497 74.898 5772 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.49 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.15), residues: 1936 helix: -2.69 (0.10), residues: 1448 sheet: None (None), residues: 0 loop : -1.88 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 518 TYR 0.062 0.005 TYR B 184 PHE 0.021 0.003 PHE B 279 TRP 0.044 0.005 TRP D 392 HIS 0.012 0.004 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.01170 (16044) covalent geometry : angle 1.22608 (21680) hydrogen bonds : bond 0.13900 ( 1097) hydrogen bonds : angle 7.27441 ( 3243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 619 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 619 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8414 (mmt) cc_final: 0.8201 (tpt) REVERT: A 261 GLU cc_start: 0.9313 (mp0) cc_final: 0.9053 (mp0) REVERT: A 284 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8175 (mm-30) REVERT: A 305 TRP cc_start: 0.8259 (t60) cc_final: 0.7163 (t60) REVERT: A 520 MET cc_start: 0.9057 (ttp) cc_final: 0.8675 (ttp) REVERT: A 537 ASP cc_start: 0.8895 (t0) cc_final: 0.8425 (t0) REVERT: B 210 MET cc_start: 0.8412 (mmt) cc_final: 0.8187 (tpt) REVERT: B 261 GLU cc_start: 0.9297 (mp0) cc_final: 0.9056 (mp0) REVERT: B 290 GLU cc_start: 0.8799 (pp20) cc_final: 0.8577 (pp20) REVERT: B 305 TRP cc_start: 0.8494 (t60) cc_final: 0.7356 (t60) REVERT: B 520 MET cc_start: 0.8968 (ttp) cc_final: 0.8565 (ttp) REVERT: B 537 ASP cc_start: 0.8903 (t0) cc_final: 0.8409 (t0) REVERT: C 28 ILE cc_start: 0.8066 (mt) cc_final: 0.7426 (mm) REVERT: C 87 ARG cc_start: 0.8977 (ttm110) cc_final: 0.8701 (ttm110) REVERT: C 101 ILE cc_start: 0.9159 (pt) cc_final: 0.8925 (mp) REVERT: C 119 ASP cc_start: 0.8517 (t0) cc_final: 0.8215 (t0) REVERT: C 126 ILE cc_start: 0.9344 (mm) cc_final: 0.9092 (tt) REVERT: D 210 MET cc_start: 0.8410 (mmt) cc_final: 0.8095 (tmm) REVERT: D 261 GLU cc_start: 0.9313 (mp0) cc_final: 0.9051 (mp0) REVERT: D 284 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8157 (mm-30) REVERT: D 305 TRP cc_start: 0.8241 (t60) cc_final: 0.7147 (t60) REVERT: D 537 ASP cc_start: 0.8886 (t0) cc_final: 0.8427 (t0) REVERT: E 9 GLN cc_start: 0.8427 (mt0) cc_final: 0.7910 (mp10) REVERT: E 119 ASP cc_start: 0.8832 (t0) cc_final: 0.8519 (t0) REVERT: E 123 ASP cc_start: 0.8650 (m-30) cc_final: 0.8205 (m-30) REVERT: F 9 GLN cc_start: 0.8454 (mt0) cc_final: 0.8090 (mt0) REVERT: F 87 ARG cc_start: 0.8965 (ttm110) cc_final: 0.8603 (ttm110) REVERT: F 113 LEU cc_start: 0.9094 (mt) cc_final: 0.8887 (mt) REVERT: F 119 ASP cc_start: 0.8804 (t0) cc_final: 0.8383 (t0) REVERT: F 123 ASP cc_start: 0.8621 (m-30) cc_final: 0.8330 (m-30) REVERT: G 210 MET cc_start: 0.8452 (mmt) cc_final: 0.8212 (tpt) REVERT: G 261 GLU cc_start: 0.9297 (mp0) cc_final: 0.9046 (mp0) REVERT: G 290 GLU cc_start: 0.8757 (pp20) cc_final: 0.8502 (pp20) REVERT: G 305 TRP cc_start: 0.8473 (t60) cc_final: 0.7336 (t60) REVERT: G 520 MET cc_start: 0.9031 (ttp) cc_final: 0.8784 (ttp) REVERT: G 537 ASP cc_start: 0.8940 (t0) cc_final: 0.8484 (t0) REVERT: H 101 ILE cc_start: 0.9060 (pt) cc_final: 0.8781 (mp) outliers start: 0 outliers final: 0 residues processed: 619 average time/residue: 0.4146 time to fit residues: 339.0725 Evaluate side-chains 402 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 544 GLN G 544 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.133068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098823 restraints weight = 128999.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.103110 restraints weight = 53448.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.105655 restraints weight = 32983.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.107150 restraints weight = 25404.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.107642 restraints weight = 21850.460| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16044 Z= 0.137 Angle : 0.572 6.701 21680 Z= 0.312 Chirality : 0.036 0.119 2428 Planarity : 0.004 0.065 2732 Dihedral : 4.615 20.466 2148 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.64 % Allowed : 11.17 % Favored : 87.20 % 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 are not related in a simple way. whole: -1.20 (0.17), residues: 1936 helix: -0.60 (0.12), residues: 1468 sheet: None (None), residues: 0 loop : -0.88 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 174 TYR 0.022 0.001 TYR G 545 PHE 0.018 0.001 PHE H 69 TRP 0.022 0.002 TRP A 120 HIS 0.004 0.001 HIS C 108 Details of bonding type rmsd covalent geometry : bond 0.00283 (16044) covalent geometry : angle 0.57205 (21680) hydrogen bonds : bond 0.04807 ( 1097) hydrogen bonds : angle 5.17070 ( 3243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 542 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 515 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 PHE cc_start: 0.8223 (t80) cc_final: 0.7966 (t80) REVERT: A 210 MET cc_start: 0.8269 (mmt) cc_final: 0.7753 (tmm) REVERT: A 520 MET cc_start: 0.8850 (ttp) cc_final: 0.8443 (ttp) REVERT: A 540 ASP cc_start: 0.9391 (m-30) cc_final: 0.9117 (m-30) REVERT: B 123 PHE cc_start: 0.8159 (t80) cc_final: 0.7890 (t80) REVERT: B 124 VAL cc_start: 0.8268 (t) cc_final: 0.8025 (p) REVERT: B 210 MET cc_start: 0.8271 (mmt) cc_final: 0.7741 (tmm) REVERT: B 284 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7891 (mm-30) REVERT: B 520 MET cc_start: 0.8950 (ttp) cc_final: 0.8491 (ttp) REVERT: C 72 MET cc_start: 0.8745 (tmm) cc_final: 0.8336 (tmm) REVERT: C 110 MET cc_start: 0.9350 (mmp) cc_final: 0.9088 (mmp) REVERT: C 126 ILE cc_start: 0.9275 (mm) cc_final: 0.9023 (tt) REVERT: C 145 MET cc_start: 0.9027 (ttm) cc_final: 0.8796 (ttp) REVERT: D 123 PHE cc_start: 0.8256 (t80) cc_final: 0.8001 (t80) REVERT: D 210 MET cc_start: 0.8266 (mmt) cc_final: 0.7751 (tmm) REVERT: D 540 ASP cc_start: 0.9400 (m-30) cc_final: 0.9114 (m-30) REVERT: E 49 LEU cc_start: 0.8945 (mt) cc_final: 0.8586 (mt) REVERT: E 50 GLN cc_start: 0.9467 (tp40) cc_final: 0.9213 (tp40) REVERT: E 72 MET cc_start: 0.8714 (tmm) cc_final: 0.8461 (tmm) REVERT: E 75 ARG cc_start: 0.8206 (ptp90) cc_final: 0.7706 (ptt90) REVERT: E 119 ASP cc_start: 0.8698 (t0) cc_final: 0.8459 (t0) REVERT: F 50 GLN cc_start: 0.9446 (tp40) cc_final: 0.9197 (tm-30) REVERT: F 110 MET cc_start: 0.9378 (mmp) cc_final: 0.9091 (mmp) REVERT: F 119 ASP cc_start: 0.8607 (t0) cc_final: 0.8372 (t0) REVERT: F 145 MET cc_start: 0.9057 (ttm) cc_final: 0.8731 (ttp) REVERT: G 123 PHE cc_start: 0.8204 (t80) cc_final: 0.7970 (t80) REVERT: G 210 MET cc_start: 0.8250 (mmt) cc_final: 0.7721 (tmm) REVERT: G 284 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7860 (mm-30) REVERT: G 520 MET cc_start: 0.8935 (ttp) cc_final: 0.8489 (ttp) REVERT: H 29 THR cc_start: 0.8910 (m) cc_final: 0.8685 (p) REVERT: H 49 LEU cc_start: 0.9080 (mt) cc_final: 0.8739 (mt) REVERT: H 50 GLN cc_start: 0.9267 (tp40) cc_final: 0.9029 (tp-100) REVERT: H 72 MET cc_start: 0.8840 (tmm) cc_final: 0.8615 (tmm) REVERT: H 75 ARG cc_start: 0.8021 (ptp90) cc_final: 0.7561 (ptt90) REVERT: H 119 ASP cc_start: 0.8934 (t0) cc_final: 0.8237 (t0) outliers start: 27 outliers final: 21 residues processed: 527 average time/residue: 0.4065 time to fit residues: 285.6340 Evaluate side-chains 442 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 421 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain G residue 125 TYR Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 552 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 521 GLN C 112 ASN E 112 ASN F 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.127749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.092973 restraints weight = 128840.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.096793 restraints weight = 55449.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.099106 restraints weight = 34994.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.100467 restraints weight = 27199.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.101076 restraints weight = 23672.456| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16044 Z= 0.241 Angle : 0.590 5.485 21680 Z= 0.332 Chirality : 0.036 0.111 2428 Planarity : 0.004 0.045 2732 Dihedral : 4.357 20.106 2148 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.79 % Allowed : 15.11 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.18), residues: 1936 helix: 0.20 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.64 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 519 TYR 0.016 0.002 TYR G 545 PHE 0.017 0.002 PHE G 270 TRP 0.020 0.002 TRP B 120 HIS 0.004 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00491 (16044) covalent geometry : angle 0.58970 (21680) hydrogen bonds : bond 0.04668 ( 1097) hydrogen bonds : angle 5.12648 ( 3243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 449 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 403 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8830 (pt0) cc_final: 0.8603 (pp30) REVERT: B 123 PHE cc_start: 0.8310 (t80) cc_final: 0.8088 (t80) REVERT: B 124 VAL cc_start: 0.8393 (t) cc_final: 0.8116 (p) REVERT: B 243 ARG cc_start: 0.5855 (tpm170) cc_final: 0.5490 (tpp-160) REVERT: B 284 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7809 (mm-30) REVERT: B 520 MET cc_start: 0.8909 (ttp) cc_final: 0.8508 (ttp) REVERT: C 72 MET cc_start: 0.8809 (tmm) cc_final: 0.8438 (tmm) REVERT: E 38 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.8907 (ptp-110) REVERT: E 50 GLN cc_start: 0.9437 (tp40) cc_final: 0.9203 (tp40) REVERT: E 75 ARG cc_start: 0.8222 (ptp90) cc_final: 0.7723 (ptt90) REVERT: E 125 MET cc_start: 0.8794 (ttt) cc_final: 0.8515 (ttt) REVERT: F 38 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8936 (ptp-110) REVERT: F 50 GLN cc_start: 0.9394 (tp40) cc_final: 0.9185 (tm-30) REVERT: F 72 MET cc_start: 0.8795 (tmm) cc_final: 0.8284 (tmm) REVERT: G 124 VAL cc_start: 0.8383 (t) cc_final: 0.8182 (p) REVERT: G 520 MET cc_start: 0.8899 (ttp) cc_final: 0.8476 (ttp) REVERT: H 73 MET cc_start: 0.8719 (mmm) cc_final: 0.8511 (mmm) REVERT: H 75 ARG cc_start: 0.8072 (ptp90) cc_final: 0.7607 (ptt90) REVERT: H 100 TYR cc_start: 0.9013 (m-80) cc_final: 0.8326 (m-80) REVERT: H 113 LEU cc_start: 0.9146 (mt) cc_final: 0.8600 (tp) outliers start: 46 outliers final: 44 residues processed: 428 average time/residue: 0.3876 time to fit residues: 225.1578 Evaluate side-chains 415 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 369 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain D residue 125 TYR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain G residue 125 TYR Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 552 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 94 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 HIS F 108 HIS H 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.125409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.090392 restraints weight = 129712.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.094082 restraints weight = 56267.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096392 restraints weight = 35993.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.097465 restraints weight = 27927.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098388 restraints weight = 24828.706| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16044 Z= 0.285 Angle : 0.610 5.635 21680 Z= 0.346 Chirality : 0.036 0.112 2428 Planarity : 0.004 0.043 2732 Dihedral : 4.371 20.334 2148 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.19 % Allowed : 16.69 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.19), residues: 1936 helix: 0.34 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.68 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 533 TYR 0.019 0.002 TYR A 184 PHE 0.017 0.002 PHE E 69 TRP 0.014 0.002 TRP G 176 HIS 0.003 0.001 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00572 (16044) covalent geometry : angle 0.61034 (21680) hydrogen bonds : bond 0.04628 ( 1097) hydrogen bonds : angle 5.11925 ( 3243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 476 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 407 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8814 (tp30) cc_final: 0.8311 (mp0) REVERT: A 520 MET cc_start: 0.8814 (ttp) cc_final: 0.8450 (ttp) REVERT: B 359 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8556 (mp10) REVERT: B 520 MET cc_start: 0.8929 (ttp) cc_final: 0.8545 (ttp) REVERT: C 72 MET cc_start: 0.8837 (tmm) cc_final: 0.8585 (tmm) REVERT: C 73 MET cc_start: 0.8289 (mmm) cc_final: 0.8029 (mmm) REVERT: C 100 TYR cc_start: 0.9253 (m-80) cc_final: 0.8659 (m-80) REVERT: C 113 LEU cc_start: 0.9112 (mt) cc_final: 0.8542 (tp) REVERT: E 50 GLN cc_start: 0.9414 (tp40) cc_final: 0.9172 (tp40) REVERT: E 75 ARG cc_start: 0.8208 (ptp90) cc_final: 0.7652 (ptt90) REVERT: E 125 MET cc_start: 0.9015 (ttt) cc_final: 0.8737 (ttt) REVERT: F 72 MET cc_start: 0.8932 (tmm) cc_final: 0.8696 (tmm) REVERT: F 87 ARG cc_start: 0.9010 (ttm110) cc_final: 0.8772 (mtt90) REVERT: F 145 MET cc_start: 0.9118 (ttm) cc_final: 0.8895 (ttp) REVERT: G 520 MET cc_start: 0.8932 (ttp) cc_final: 0.8530 (ttp) REVERT: H 9 GLN cc_start: 0.8324 (mt0) cc_final: 0.7792 (mp10) REVERT: H 87 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8026 (mtt90) outliers start: 69 outliers final: 60 residues processed: 446 average time/residue: 0.3795 time to fit residues: 230.5893 Evaluate side-chains 423 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 361 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 381 CYS Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 514 ILE Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 138 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 123 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 148 optimal weight: 0.0370 chunk 105 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.127488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.092684 restraints weight = 130278.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.096596 restraints weight = 54569.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.098952 restraints weight = 34191.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.100407 restraints weight = 26362.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.100954 restraints weight = 22812.214| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16044 Z= 0.145 Angle : 0.548 7.531 21680 Z= 0.295 Chirality : 0.034 0.108 2428 Planarity : 0.003 0.042 2732 Dihedral : 4.090 19.297 2148 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.09 % Allowed : 18.75 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 1936 helix: 0.94 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.26 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 533 TYR 0.012 0.001 TYR A 184 PHE 0.022 0.001 PHE G 270 TRP 0.011 0.001 TRP B 120 HIS 0.004 0.001 HIS G 363 Details of bonding type rmsd covalent geometry : bond 0.00294 (16044) covalent geometry : angle 0.54777 (21680) hydrogen bonds : bond 0.04154 ( 1097) hydrogen bonds : angle 4.55771 ( 3243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 472 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 421 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8806 (tp30) cc_final: 0.8281 (mp0) REVERT: A 301 ASP cc_start: 0.8462 (m-30) cc_final: 0.8261 (m-30) REVERT: A 520 MET cc_start: 0.8774 (ttp) cc_final: 0.8426 (ttp) REVERT: B 359 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8507 (mp10) REVERT: B 520 MET cc_start: 0.8856 (ttp) cc_final: 0.8435 (ttp) REVERT: B 527 LYS cc_start: 0.9629 (tmtt) cc_final: 0.9419 (ttpp) REVERT: B 528 LYS cc_start: 0.9466 (tppt) cc_final: 0.9256 (tppt) REVERT: C 87 ARG cc_start: 0.9010 (ttm110) cc_final: 0.8761 (mtt90) REVERT: C 113 LEU cc_start: 0.9097 (mt) cc_final: 0.8618 (tp) REVERT: D 115 GLU cc_start: 0.8834 (tp30) cc_final: 0.8219 (mp0) REVERT: D 301 ASP cc_start: 0.8466 (m-30) cc_final: 0.8252 (m-30) REVERT: D 359 GLN cc_start: 0.8903 (tp40) cc_final: 0.8517 (mp10) REVERT: E 50 GLN cc_start: 0.9391 (tp40) cc_final: 0.9104 (tp40) REVERT: E 72 MET cc_start: 0.8792 (tmm) cc_final: 0.8539 (tmm) REVERT: E 100 TYR cc_start: 0.9114 (m-80) cc_final: 0.8594 (m-80) REVERT: E 113 LEU cc_start: 0.9099 (mt) cc_final: 0.8590 (tp) REVERT: F 87 ARG cc_start: 0.9020 (ttm110) cc_final: 0.8755 (mtt90) REVERT: F 113 LEU cc_start: 0.9069 (mt) cc_final: 0.8552 (tp) REVERT: G 301 ASP cc_start: 0.8494 (m-30) cc_final: 0.8272 (m-30) REVERT: G 520 MET cc_start: 0.8838 (ttp) cc_final: 0.8409 (ttp) REVERT: G 543 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8840 (mt-10) REVERT: H 9 GLN cc_start: 0.8310 (mt0) cc_final: 0.7817 (mp10) REVERT: H 77 MET cc_start: 0.8401 (ppp) cc_final: 0.7865 (ppp) REVERT: H 113 LEU cc_start: 0.9173 (mt) cc_final: 0.8793 (tp) outliers start: 51 outliers final: 39 residues processed: 449 average time/residue: 0.3743 time to fit residues: 231.1466 Evaluate side-chains 420 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 380 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 381 CYS Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 40 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 143 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN B 234 GLN ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.125487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.090815 restraints weight = 132943.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.094656 restraints weight = 56668.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.097000 restraints weight = 35766.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098250 restraints weight = 27793.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.098814 restraints weight = 24359.534| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.6807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16044 Z= 0.245 Angle : 0.597 8.824 21680 Z= 0.333 Chirality : 0.035 0.111 2428 Planarity : 0.004 0.046 2732 Dihedral : 4.215 20.726 2148 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.58 % Allowed : 20.33 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 1936 helix: 0.75 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.30 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 533 TYR 0.011 0.001 TYR G 545 PHE 0.022 0.002 PHE H 93 TRP 0.010 0.001 TRP D 176 HIS 0.004 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00496 (16044) covalent geometry : angle 0.59730 (21680) hydrogen bonds : bond 0.04380 ( 1097) hydrogen bonds : angle 4.80119 ( 3243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 444 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 385 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8749 (tp30) cc_final: 0.8209 (mp0) REVERT: B 359 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8558 (mp10) REVERT: D 115 GLU cc_start: 0.8758 (tp30) cc_final: 0.8119 (mp0) REVERT: D 359 GLN cc_start: 0.8993 (tp40) cc_final: 0.8564 (mp10) REVERT: E 50 GLN cc_start: 0.9375 (tp40) cc_final: 0.9128 (tp40) REVERT: E 100 TYR cc_start: 0.9189 (m-80) cc_final: 0.8612 (m-80) REVERT: E 113 LEU cc_start: 0.9080 (mt) cc_final: 0.8562 (tp) REVERT: F 50 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8887 (tm-30) REVERT: G 543 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8866 (mt-10) REVERT: H 9 GLN cc_start: 0.8342 (mt0) cc_final: 0.7806 (mp10) outliers start: 59 outliers final: 51 residues processed: 418 average time/residue: 0.3689 time to fit residues: 210.2348 Evaluate side-chains 423 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 371 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 381 CYS Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 20 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 189 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 234 GLN ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.129067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.094624 restraints weight = 129049.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.098627 restraints weight = 54111.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.101074 restraints weight = 33798.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.102421 restraints weight = 26125.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.103054 restraints weight = 22719.761| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.6988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16044 Z= 0.116 Angle : 0.550 8.266 21680 Z= 0.290 Chirality : 0.034 0.118 2428 Planarity : 0.003 0.059 2732 Dihedral : 3.933 19.033 2148 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.37 % Allowed : 22.21 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.19), residues: 1936 helix: 1.27 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : 0.20 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 533 TYR 0.009 0.001 TYR A 545 PHE 0.022 0.001 PHE H 93 TRP 0.008 0.001 TRP G 120 HIS 0.004 0.001 HIS G 363 Details of bonding type rmsd covalent geometry : bond 0.00247 (16044) covalent geometry : angle 0.55002 (21680) hydrogen bonds : bond 0.03780 ( 1097) hydrogen bonds : angle 4.20871 ( 3243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 472 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 433 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8713 (tp30) cc_final: 0.8216 (mp0) REVERT: A 331 CYS cc_start: 0.9084 (m) cc_final: 0.8868 (m) REVERT: A 559 LEU cc_start: 0.8095 (mt) cc_final: 0.7749 (tt) REVERT: B 259 ARG cc_start: 0.8788 (ptt-90) cc_final: 0.8292 (ptp90) REVERT: B 359 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8539 (mp10) REVERT: B 527 LYS cc_start: 0.9610 (tmtt) cc_final: 0.9391 (ttpp) REVERT: C 87 ARG cc_start: 0.9009 (ttm110) cc_final: 0.8756 (mtt90) REVERT: D 115 GLU cc_start: 0.8724 (tp30) cc_final: 0.8125 (mp0) REVERT: D 359 GLN cc_start: 0.8954 (tp40) cc_final: 0.8543 (mp10) REVERT: D 527 LYS cc_start: 0.9589 (tmtt) cc_final: 0.9301 (ttpp) REVERT: D 528 LYS cc_start: 0.9488 (tppt) cc_final: 0.9224 (tppt) REVERT: E 50 GLN cc_start: 0.9375 (tp40) cc_final: 0.9083 (tp40) REVERT: E 91 ARG cc_start: 0.8921 (mtt90) cc_final: 0.8311 (mtt-85) REVERT: E 100 TYR cc_start: 0.9270 (m-80) cc_final: 0.8748 (m-80) REVERT: E 113 LEU cc_start: 0.9120 (mt) cc_final: 0.8625 (tp) REVERT: F 50 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8804 (tm-30) REVERT: F 100 TYR cc_start: 0.9315 (m-80) cc_final: 0.8589 (m-80) REVERT: F 113 LEU cc_start: 0.9085 (mt) cc_final: 0.8632 (tp) REVERT: F 145 MET cc_start: 0.8939 (ttp) cc_final: 0.8687 (ttp) REVERT: G 261 GLU cc_start: 0.9217 (mp0) cc_final: 0.8993 (mp0) REVERT: G 543 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8819 (mt-10) REVERT: H 9 GLN cc_start: 0.8330 (mt0) cc_final: 0.7815 (mp10) REVERT: H 77 MET cc_start: 0.8350 (ppp) cc_final: 0.7828 (ppp) REVERT: H 100 TYR cc_start: 0.9082 (m-80) cc_final: 0.8469 (m-80) REVERT: H 113 LEU cc_start: 0.9173 (mt) cc_final: 0.8828 (tp) outliers start: 39 outliers final: 31 residues processed: 450 average time/residue: 0.3588 time to fit residues: 222.5936 Evaluate side-chains 417 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 385 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 520 MET Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain H residue 20 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 155 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.126562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.091925 restraints weight = 130761.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095735 restraints weight = 55524.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.098020 restraints weight = 35170.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.099319 restraints weight = 27452.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.099881 restraints weight = 23895.157| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.7195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16044 Z= 0.205 Angle : 0.572 6.007 21680 Z= 0.318 Chirality : 0.035 0.136 2428 Planarity : 0.004 0.060 2732 Dihedral : 3.998 18.638 2148 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.67 % Allowed : 24.03 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.19), residues: 1936 helix: 1.12 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.29 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 533 TYR 0.013 0.001 TYR G 545 PHE 0.025 0.001 PHE H 69 TRP 0.008 0.001 TRP A 392 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00415 (16044) covalent geometry : angle 0.57236 (21680) hydrogen bonds : bond 0.04033 ( 1097) hydrogen bonds : angle 4.51993 ( 3243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 433 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 389 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8713 (tp30) cc_final: 0.8229 (mp0) REVERT: A 130 PHE cc_start: 0.6911 (m-80) cc_final: 0.6478 (m-10) REVERT: B 359 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8559 (mp10) REVERT: C 87 ARG cc_start: 0.9039 (ttm110) cc_final: 0.8753 (mtt90) REVERT: C 110 MET cc_start: 0.9498 (mmp) cc_final: 0.9253 (mmp) REVERT: D 115 GLU cc_start: 0.8704 (tp30) cc_final: 0.8104 (mp0) REVERT: D 130 PHE cc_start: 0.6833 (m-80) cc_final: 0.6439 (m-80) REVERT: D 527 LYS cc_start: 0.9607 (tmtt) cc_final: 0.9378 (ttpp) REVERT: D 528 LYS cc_start: 0.9489 (tppt) cc_final: 0.9285 (tppt) REVERT: E 50 GLN cc_start: 0.9368 (tp40) cc_final: 0.9110 (tp40) REVERT: E 100 TYR cc_start: 0.9247 (m-80) cc_final: 0.8653 (m-80) REVERT: E 113 LEU cc_start: 0.9117 (mt) cc_final: 0.8630 (tp) REVERT: E 125 MET cc_start: 0.8898 (ttp) cc_final: 0.8681 (ttp) REVERT: F 50 GLN cc_start: 0.9166 (tm-30) cc_final: 0.8863 (tm-30) REVERT: F 110 MET cc_start: 0.9525 (mmp) cc_final: 0.9223 (mmp) REVERT: F 113 LEU cc_start: 0.9139 (mt) cc_final: 0.8621 (tp) REVERT: G 528 LYS cc_start: 0.9297 (tppt) cc_final: 0.9035 (tppt) REVERT: G 543 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8856 (mt-10) REVERT: H 9 GLN cc_start: 0.8377 (mt0) cc_final: 0.7823 (mp10) REVERT: H 77 MET cc_start: 0.8394 (ppp) cc_final: 0.7930 (ppp) REVERT: H 100 TYR cc_start: 0.9109 (m-80) cc_final: 0.8431 (m-80) REVERT: H 113 LEU cc_start: 0.9162 (mt) cc_final: 0.8803 (tp) outliers start: 44 outliers final: 40 residues processed: 412 average time/residue: 0.3838 time to fit residues: 216.9348 Evaluate side-chains 417 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 376 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 130 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 100 optimal weight: 0.3980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.128614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093524 restraints weight = 128943.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.097420 restraints weight = 55103.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.099857 restraints weight = 34930.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.101325 restraints weight = 27072.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.101930 restraints weight = 23482.826| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.7345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16044 Z= 0.123 Angle : 0.559 9.420 21680 Z= 0.296 Chirality : 0.034 0.116 2428 Planarity : 0.004 0.082 2732 Dihedral : 3.853 18.404 2148 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.06 % Allowed : 24.64 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.19), residues: 1936 helix: 1.39 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : 0.05 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 243 TYR 0.010 0.001 TYR G 545 PHE 0.024 0.001 PHE E 93 TRP 0.007 0.001 TRP G 120 HIS 0.002 0.001 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00262 (16044) covalent geometry : angle 0.55891 (21680) hydrogen bonds : bond 0.03751 ( 1097) hydrogen bonds : angle 4.19210 ( 3243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 446 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 412 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8684 (tp30) cc_final: 0.8235 (mp0) REVERT: A 130 PHE cc_start: 0.6830 (m-80) cc_final: 0.6519 (m-80) REVERT: A 331 CYS cc_start: 0.9111 (m) cc_final: 0.8905 (m) REVERT: A 537 ASP cc_start: 0.9420 (t0) cc_final: 0.9076 (t0) REVERT: B 359 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8562 (mp10) REVERT: B 543 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8803 (mt-10) REVERT: C 87 ARG cc_start: 0.9010 (ttm110) cc_final: 0.8756 (mtt90) REVERT: C 113 LEU cc_start: 0.9153 (mt) cc_final: 0.8771 (tp) REVERT: D 115 GLU cc_start: 0.8652 (tp30) cc_final: 0.8074 (mp0) REVERT: D 130 PHE cc_start: 0.6848 (m-80) cc_final: 0.6547 (m-80) REVERT: D 527 LYS cc_start: 0.9594 (tmtt) cc_final: 0.9335 (ttpp) REVERT: D 528 LYS cc_start: 0.9485 (tppt) cc_final: 0.9272 (tppt) REVERT: E 50 GLN cc_start: 0.9375 (tp40) cc_final: 0.9098 (tp40) REVERT: E 91 ARG cc_start: 0.8920 (mtt90) cc_final: 0.8295 (mtt-85) REVERT: E 100 TYR cc_start: 0.9289 (m-80) cc_final: 0.8686 (m-80) REVERT: E 113 LEU cc_start: 0.9150 (mt) cc_final: 0.8666 (tp) REVERT: E 125 MET cc_start: 0.8821 (ttp) cc_final: 0.8606 (ttp) REVERT: F 50 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8847 (tm-30) REVERT: F 113 LEU cc_start: 0.9119 (mt) cc_final: 0.8666 (tp) REVERT: G 290 GLU cc_start: 0.8991 (pp20) cc_final: 0.8776 (pp20) REVERT: G 528 LYS cc_start: 0.9301 (tppt) cc_final: 0.9019 (tppt) REVERT: G 543 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8822 (mt-10) REVERT: H 9 GLN cc_start: 0.8345 (mt0) cc_final: 0.7827 (mp10) REVERT: H 77 MET cc_start: 0.8451 (ppp) cc_final: 0.7930 (ppp) REVERT: H 100 TYR cc_start: 0.9120 (m-80) cc_final: 0.8634 (m-80) REVERT: H 113 LEU cc_start: 0.9175 (mt) cc_final: 0.8827 (tp) outliers start: 34 outliers final: 30 residues processed: 429 average time/residue: 0.3784 time to fit residues: 223.1050 Evaluate side-chains 422 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 391 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 101 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 100 optimal weight: 0.1980 chunk 116 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 165 optimal weight: 0.1980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.129033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.094047 restraints weight = 128431.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.098002 restraints weight = 54936.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.100484 restraints weight = 34854.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.101633 restraints weight = 27005.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.102489 restraints weight = 23896.390| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.7482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16044 Z= 0.117 Angle : 0.578 7.259 21680 Z= 0.304 Chirality : 0.034 0.112 2428 Planarity : 0.004 0.081 2732 Dihedral : 3.794 19.207 2148 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.00 % Allowed : 25.49 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.19), residues: 1936 helix: 1.54 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : 0.20 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 533 TYR 0.010 0.001 TYR H 100 PHE 0.025 0.001 PHE E 93 TRP 0.006 0.001 TRP G 120 HIS 0.002 0.001 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00254 (16044) covalent geometry : angle 0.57802 (21680) hydrogen bonds : bond 0.03666 ( 1097) hydrogen bonds : angle 4.09339 ( 3243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 440 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 407 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8702 (tp30) cc_final: 0.8203 (mp0) REVERT: A 130 PHE cc_start: 0.6843 (m-80) cc_final: 0.6402 (m-80) REVERT: A 537 ASP cc_start: 0.9413 (t0) cc_final: 0.9106 (t0) REVERT: B 130 PHE cc_start: 0.6968 (m-80) cc_final: 0.6595 (m-10) REVERT: B 359 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8570 (mp10) REVERT: B 543 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8784 (mt-10) REVERT: C 87 ARG cc_start: 0.8997 (ttm110) cc_final: 0.8759 (mtt90) REVERT: C 113 LEU cc_start: 0.9148 (mt) cc_final: 0.8776 (tp) REVERT: D 115 GLU cc_start: 0.8680 (tp30) cc_final: 0.8051 (mp0) REVERT: D 130 PHE cc_start: 0.6836 (m-80) cc_final: 0.6533 (m-80) REVERT: D 527 LYS cc_start: 0.9582 (tmtt) cc_final: 0.9326 (ttpp) REVERT: D 528 LYS cc_start: 0.9471 (tppt) cc_final: 0.9255 (tppt) REVERT: E 50 GLN cc_start: 0.9367 (tp40) cc_final: 0.9092 (tp40) REVERT: E 91 ARG cc_start: 0.8920 (mtt90) cc_final: 0.8285 (mtt-85) REVERT: E 100 TYR cc_start: 0.9286 (m-80) cc_final: 0.8681 (m-80) REVERT: E 113 LEU cc_start: 0.9134 (mt) cc_final: 0.8658 (tp) REVERT: F 50 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8821 (tm-30) REVERT: F 113 LEU cc_start: 0.9112 (mt) cc_final: 0.8671 (tp) REVERT: G 130 PHE cc_start: 0.6774 (m-80) cc_final: 0.6365 (m-10) REVERT: G 290 GLU cc_start: 0.8977 (pp20) cc_final: 0.8771 (pp20) REVERT: G 528 LYS cc_start: 0.9293 (tppt) cc_final: 0.8999 (tppt) REVERT: G 543 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8808 (mt-10) REVERT: H 77 MET cc_start: 0.8455 (ppp) cc_final: 0.8031 (ppp) REVERT: H 113 LEU cc_start: 0.9180 (mt) cc_final: 0.8859 (tp) outliers start: 33 outliers final: 29 residues processed: 426 average time/residue: 0.3844 time to fit residues: 225.4800 Evaluate side-chains 421 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 391 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain H residue 20 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 187 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.128442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.093044 restraints weight = 128713.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.096908 restraints weight = 55397.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.099336 restraints weight = 35606.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.100677 restraints weight = 27932.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101249 restraints weight = 24436.607| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.7597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16044 Z= 0.134 Angle : 0.575 7.873 21680 Z= 0.307 Chirality : 0.034 0.144 2428 Planarity : 0.004 0.075 2732 Dihedral : 3.779 20.212 2148 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.12 % Allowed : 25.73 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.19), residues: 1936 helix: 1.58 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : 0.05 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 533 TYR 0.009 0.001 TYR G 545 PHE 0.027 0.001 PHE E 93 TRP 0.006 0.001 TRP D 379 HIS 0.003 0.001 HIS G 258 Details of bonding type rmsd covalent geometry : bond 0.00286 (16044) covalent geometry : angle 0.57544 (21680) hydrogen bonds : bond 0.03720 ( 1097) hydrogen bonds : angle 4.15986 ( 3243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7132.47 seconds wall clock time: 121 minutes 53.42 seconds (7313.42 seconds total)