Starting phenix.real_space_refine on Fri Jun 27 01:45:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xni_33316/06_2025/7xni_33316_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xni_33316/06_2025/7xni_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xni_33316/06_2025/7xni_33316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xni_33316/06_2025/7xni_33316.map" model { file = "/net/cci-nas-00/data/ceres_data/7xni_33316/06_2025/7xni_33316_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xni_33316/06_2025/7xni_33316_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.93, per 1000 atoms: 0.44 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: 8.19 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.08 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: 10.94 Time building geometry restraints manager: 9.98 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: 0.14 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: 0.580 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: 0.520 Extract box with map and model: 1.220 Check model and map are aligned: 0.210 Set scattering table: 0.310 Process input model: 62.160 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.130 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.340 ------------------------------------------------------------------------------- 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 : 20.98 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.044 0.005 TRP D 392 HIS 0.012 0.004 HIS B 126 PHE 0.021 0.003 PHE B 279 TYR 0.062 0.005 TYR B 184 ARG 0.006 0.001 ARG G 518 Details of bonding type rmsd hydrogen bonds : bond 0.13900 ( 1097) hydrogen bonds : angle 7.27441 ( 3243) covalent geometry : bond 0.01170 (16044) covalent geometry : angle 1.22608 (21680) *********************** 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 : 2.490 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: A 210 MET cc_start: 0.8414 (mmt) cc_final: 0.8200 (tpt) REVERT: A 261 GLU cc_start: 0.9313 (mp0) cc_final: 0.9054 (mp0) REVERT: A 284 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8176 (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: 0.8677 (ttp) REVERT: A 537 ASP cc_start: 0.8895 (t0) cc_final: 0.8424 (t0) REVERT: B 210 MET cc_start: 0.8412 (mmt) cc_final: 0.8186 (tpt) REVERT: B 261 GLU cc_start: 0.9297 (mp0) cc_final: 0.9057 (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: 0.8429 (t0) REVERT: C 28 ILE cc_start: 0.8066 (mt) cc_final: 0.7400 (mm) REVERT: C 87 ARG cc_start: 0.8977 (ttm110) cc_final: 0.8736 (ttm110) REVERT: C 101 ILE cc_start: 0.9158 (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: 0.9091 (tt) REVERT: D 210 MET cc_start: 0.8410 (mmt) cc_final: 0.8094 (tmm) REVERT: D 261 GLU cc_start: 0.9313 (mp0) cc_final: 0.9052 (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: 0.8423 (t0) REVERT: E 9 GLN cc_start: 0.8427 (mt0) cc_final: 0.7931 (mp10) REVERT: E 119 ASP cc_start: 0.8832 (t0) cc_final: 0.8518 (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: 0.8964 (ttm110) cc_final: 0.8614 (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: 0.8331 (m-30) REVERT: G 210 MET cc_start: 0.8452 (mmt) cc_final: 0.8211 (tpt) REVERT: G 261 GLU cc_start: 0.9297 (mp0) cc_final: 0.9047 (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: 0.7337 (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: 0.8779 (mp) outliers start: 0 outliers final: 0 residues processed: 619 average time/residue: 0.8843 time to fit residues: 728.6939 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 : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 GLN C 112 ASN ** D 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 GLN E 112 ASN F 112 ASN ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 544 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.132485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.098471 restraints weight = 127997.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.102736 restraints weight = 53080.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.105265 restraints weight = 32855.809| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16044 Z= 0.150 Angle : 0.587 6.576 21680 Z= 0.321 Chirality : 0.036 0.118 2428 Planarity : 0.004 0.066 2732 Dihedral : 4.627 20.675 2148 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.64 % Allowed : 11.83 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.17), residues: 1936 helix: -0.67 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : -0.91 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 120 HIS 0.005 0.001 HIS C 108 PHE 0.019 0.002 PHE H 69 TYR 0.026 0.001 TYR G 545 ARG 0.004 0.001 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.04941 ( 1097) hydrogen bonds : angle 5.17607 ( 3243) covalent geometry : bond 0.00305 (16044) covalent geometry : angle 0.58720 (21680) *********************** 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 531 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 504 time to evaluate : 2.566 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: A 123 PHE cc_start: 0.8267 (t80) cc_final: 0.8005 (t80) REVERT: A 210 MET cc_start: 0.8277 (mmt) cc_final: 0.7763 (tmm) REVERT: A 520 MET cc_start: 0.8859 (ttp) cc_final: 0.8425 (ttp) REVERT: A 540 ASP cc_start: 0.9402 (m-30) cc_final: 0.9134 (m-30) REVERT: B 123 PHE cc_start: 0.8202 (t80) cc_final: 0.7955 (t80) REVERT: B 210 MET cc_start: 0.8281 (mmt) cc_final: 0.7756 (tmm) REVERT: B 520 MET cc_start: 0.8965 (ttp) cc_final: 0.8534 (ttp) REVERT: C 50 GLN cc_start: 0.9409 (tp40) cc_final: 0.9048 (tm-30) REVERT: C 72 MET cc_start: 0.8732 (tmm) cc_final: 0.8363 (tmm) REVERT: C 83 GLU cc_start: 0.9125 (tt0) cc_final: 0.8674 (mm-30) REVERT: C 110 MET cc_start: 0.9358 (mmp) cc_final: 0.9124 (mmp) REVERT: C 126 ILE cc_start: 0.9293 (mm) cc_final: 0.9039 (tt) REVERT: C 145 MET cc_start: 0.9060 (ttm) cc_final: 0.8821 (ttp) REVERT: D 123 PHE cc_start: 0.8290 (t80) cc_final: 0.8031 (t80) REVERT: D 210 MET cc_start: 0.8275 (mmt) cc_final: 0.7766 (tmm) REVERT: D 540 ASP cc_start: 0.9415 (m-30) cc_final: 0.9131 (m-30) REVERT: D 544 GLN cc_start: 0.8804 (pp30) cc_final: 0.8579 (pp30) REVERT: E 49 LEU cc_start: 0.8970 (mt) cc_final: 0.8602 (mt) REVERT: E 50 GLN cc_start: 0.9463 (tp40) cc_final: 0.9207 (tp40) REVERT: E 75 ARG cc_start: 0.8218 (ptp90) cc_final: 0.7768 (ptt90) REVERT: E 100 TYR cc_start: 0.8582 (m-80) cc_final: 0.8224 (m-80) REVERT: E 119 ASP cc_start: 0.8725 (t0) cc_final: 0.8434 (t0) REVERT: E 123 ASP cc_start: 0.8526 (m-30) cc_final: 0.8256 (m-30) REVERT: F 14 LYS cc_start: 0.9384 (tppt) cc_final: 0.9143 (mttp) REVERT: F 50 GLN cc_start: 0.9444 (tp40) cc_final: 0.9223 (tm-30) REVERT: F 110 MET cc_start: 0.9367 (mmp) cc_final: 0.9101 (mmp) REVERT: F 119 ASP cc_start: 0.8645 (t0) cc_final: 0.8379 (t0) REVERT: F 145 MET cc_start: 0.9077 (ttm) cc_final: 0.8752 (ttp) REVERT: G 210 MET cc_start: 0.8304 (mmt) cc_final: 0.7786 (tmm) REVERT: G 284 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7919 (mm-30) REVERT: G 520 MET cc_start: 0.8979 (ttp) cc_final: 0.8504 (ttp) REVERT: G 540 ASP cc_start: 0.9390 (m-30) cc_final: 0.9105 (m-30) REVERT: G 543 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8977 (mt-10) REVERT: H 29 THR cc_start: 0.8883 (m) cc_final: 0.8645 (p) REVERT: H 49 LEU cc_start: 0.9075 (mt) cc_final: 0.8720 (mt) REVERT: H 72 MET cc_start: 0.8862 (tmm) cc_final: 0.8607 (tmm) REVERT: H 75 ARG cc_start: 0.8010 (ptp90) cc_final: 0.7571 (ptt90) REVERT: H 119 ASP cc_start: 0.8972 (t0) cc_final: 0.8264 (t0) REVERT: H 123 ASP cc_start: 0.9360 (t0) cc_final: 0.9140 (m-30) outliers start: 27 outliers final: 20 residues processed: 515 average time/residue: 0.8084 time to fit residues: 560.8088 Evaluate side-chains 441 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 421 time to evaluate : 2.546 ------------------------------------------------------------------------------- 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 552 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 114 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 30.0000 chunk 146 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 521 GLN H 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.129756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.094933 restraints weight = 130606.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.099005 restraints weight = 54684.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.101447 restraints weight = 34152.205| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16044 Z= 0.164 Angle : 0.550 6.646 21680 Z= 0.304 Chirality : 0.035 0.113 2428 Planarity : 0.004 0.041 2732 Dihedral : 4.243 19.383 2148 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.55 % Allowed : 15.29 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 1936 helix: 0.47 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -0.50 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 120 HIS 0.003 0.001 HIS A 126 PHE 0.017 0.001 PHE F 69 TYR 0.016 0.001 TYR G 545 ARG 0.007 0.001 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 1097) hydrogen bonds : angle 4.81975 ( 3243) covalent geometry : bond 0.00336 (16044) covalent geometry : angle 0.55041 (21680) *********************** 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 481 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 439 time to evaluate : 2.466 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: A 123 PHE cc_start: 0.8274 (t80) cc_final: 0.8015 (t80) REVERT: A 124 VAL cc_start: 0.8364 (t) cc_final: 0.8086 (p) REVERT: A 202 ASP cc_start: 0.9125 (OUTLIER) cc_final: 0.8835 (p0) REVERT: A 210 MET cc_start: 0.8224 (mmt) cc_final: 0.7643 (tmm) REVERT: B 123 PHE cc_start: 0.8259 (t80) cc_final: 0.8030 (t80) REVERT: B 124 VAL cc_start: 0.8359 (t) cc_final: 0.8091 (p) REVERT: B 159 MET cc_start: 0.8989 (tpp) cc_final: 0.8687 (ttm) REVERT: B 202 ASP cc_start: 0.9134 (OUTLIER) cc_final: 0.8834 (p0) REVERT: B 210 MET cc_start: 0.8225 (mmt) cc_final: 0.7630 (tmm) REVERT: B 520 MET cc_start: 0.8927 (ttp) cc_final: 0.8464 (ttp) REVERT: B 543 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8916 (mt-10) REVERT: C 50 GLN cc_start: 0.9457 (tp40) cc_final: 0.9059 (tm-30) REVERT: C 72 MET cc_start: 0.8705 (tmm) cc_final: 0.8467 (tmm) REVERT: C 73 MET cc_start: 0.8522 (mmm) cc_final: 0.8288 (mmm) REVERT: C 83 GLU cc_start: 0.9127 (tt0) cc_final: 0.8667 (mm-30) REVERT: C 87 ARG cc_start: 0.8920 (ttm110) cc_final: 0.8638 (mtt90) REVERT: C 113 LEU cc_start: 0.9015 (mt) cc_final: 0.8386 (tp) REVERT: C 126 ILE cc_start: 0.9298 (mm) cc_final: 0.9075 (tt) REVERT: D 123 PHE cc_start: 0.8314 (t80) cc_final: 0.8056 (t80) REVERT: D 124 VAL cc_start: 0.8360 (t) cc_final: 0.8085 (p) REVERT: D 202 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8775 (p0) REVERT: D 210 MET cc_start: 0.8231 (mmt) cc_final: 0.7654 (tmm) REVERT: E 38 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.8913 (ptp-110) REVERT: E 50 GLN cc_start: 0.9445 (tp40) cc_final: 0.9225 (tp40) REVERT: E 73 MET cc_start: 0.8634 (mmm) cc_final: 0.8429 (mmm) REVERT: E 75 ARG cc_start: 0.8305 (ptp90) cc_final: 0.7766 (ptt90) REVERT: E 113 LEU cc_start: 0.9155 (mt) cc_final: 0.8573 (tp) REVERT: E 123 ASP cc_start: 0.8473 (m-30) cc_final: 0.8142 (m-30) REVERT: F 38 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8920 (ptp-110) REVERT: F 50 GLN cc_start: 0.9419 (tp40) cc_final: 0.9189 (tm-30) REVERT: F 72 MET cc_start: 0.8833 (tmm) cc_final: 0.8605 (tmm) REVERT: G 123 PHE cc_start: 0.8235 (t80) cc_final: 0.7976 (t80) REVERT: G 124 VAL cc_start: 0.8349 (t) cc_final: 0.8076 (p) REVERT: G 159 MET cc_start: 0.9012 (tpp) cc_final: 0.8726 (ttm) REVERT: G 202 ASP cc_start: 0.9008 (OUTLIER) cc_final: 0.8611 (p0) REVERT: G 210 MET cc_start: 0.8244 (mmt) cc_final: 0.7640 (tmm) REVERT: G 284 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7767 (mm-30) REVERT: G 520 MET cc_start: 0.8876 (ttp) cc_final: 0.8425 (ttp) REVERT: G 540 ASP cc_start: 0.9346 (m-30) cc_final: 0.9019 (m-30) REVERT: H 75 ARG cc_start: 0.8018 (ptp90) cc_final: 0.7635 (ptt90) REVERT: H 100 TYR cc_start: 0.9050 (m-80) cc_final: 0.8365 (m-80) REVERT: H 113 LEU cc_start: 0.9130 (mt) cc_final: 0.8632 (tp) REVERT: H 119 ASP cc_start: 0.8994 (t0) cc_final: 0.8303 (t0) REVERT: H 123 ASP cc_start: 0.9349 (t0) cc_final: 0.9114 (m-30) outliers start: 42 outliers final: 36 residues processed: 465 average time/residue: 0.8671 time to fit residues: 559.4322 Evaluate side-chains 447 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 405 time to evaluate : 3.009 ------------------------------------------------------------------------------- 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 202 ASP 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 552 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 202 ASP Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 PHE 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 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 202 ASP 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 E residue 9 GLN Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 38 ARG 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 202 ASP 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 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 23 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** D 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.128219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.093577 restraints weight = 130670.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.097568 restraints weight = 55297.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.099926 restraints weight = 34390.859| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16044 Z= 0.176 Angle : 0.540 6.982 21680 Z= 0.297 Chirality : 0.034 0.108 2428 Planarity : 0.003 0.038 2732 Dihedral : 4.077 19.380 2148 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.76 % Allowed : 15.53 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1936 helix: 0.90 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.05 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 176 HIS 0.003 0.001 HIS B 240 PHE 0.017 0.001 PHE H 69 TYR 0.012 0.001 TYR D 184 ARG 0.009 0.001 ARG G 533 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 1097) hydrogen bonds : angle 4.63134 ( 3243) covalent geometry : bond 0.00357 (16044) covalent geometry : angle 0.53970 (21680) *********************** 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 470 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 408 time to evaluate : 2.531 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: A 202 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8776 (p0) REVERT: A 301 ASP cc_start: 0.8531 (m-30) cc_final: 0.8322 (m-30) REVERT: A 520 MET cc_start: 0.8908 (ttp) cc_final: 0.8458 (ttp) REVERT: B 202 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8776 (p0) REVERT: B 301 ASP cc_start: 0.8508 (m-30) cc_final: 0.8303 (m-30) REVERT: B 520 MET cc_start: 0.8887 (ttp) cc_final: 0.8457 (ttp) REVERT: C 50 GLN cc_start: 0.9441 (tp40) cc_final: 0.9063 (tm-30) REVERT: C 72 MET cc_start: 0.8777 (tmm) cc_final: 0.8031 (tmm) REVERT: C 73 MET cc_start: 0.8510 (mmm) cc_final: 0.8232 (mmm) REVERT: C 83 GLU cc_start: 0.9116 (tt0) cc_final: 0.8727 (mm-30) REVERT: C 110 MET cc_start: 0.9548 (mmp) cc_final: 0.9266 (mmp) REVERT: D 202 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8494 (p0) REVERT: D 301 ASP cc_start: 0.8497 (m-30) cc_final: 0.8287 (m-30) REVERT: E 38 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.8900 (ptp-110) REVERT: E 50 GLN cc_start: 0.9417 (tp40) cc_final: 0.9100 (tp-100) REVERT: E 113 LEU cc_start: 0.9159 (mt) cc_final: 0.8610 (tp) REVERT: F 50 GLN cc_start: 0.9399 (tp40) cc_final: 0.9163 (tm-30) REVERT: F 113 LEU cc_start: 0.9034 (mt) cc_final: 0.8513 (tp) REVERT: F 144 GLN cc_start: 0.9499 (mm110) cc_final: 0.9263 (mm110) REVERT: F 145 MET cc_start: 0.9020 (ttm) cc_final: 0.8783 (ttp) REVERT: G 520 MET cc_start: 0.8839 (ttp) cc_final: 0.8452 (ttp) REVERT: H 9 GLN cc_start: 0.8484 (mt0) cc_final: 0.8100 (mp10) REVERT: H 75 ARG cc_start: 0.8039 (ptp90) cc_final: 0.7529 (ptt90) REVERT: H 87 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8248 (mtt90) REVERT: H 119 ASP cc_start: 0.8972 (t0) cc_final: 0.8258 (t0) REVERT: H 125 MET cc_start: 0.8755 (ttp) cc_final: 0.8553 (ttp) outliers start: 62 outliers final: 45 residues processed: 441 average time/residue: 0.7804 time to fit residues: 469.5406 Evaluate side-chains 429 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 379 time to evaluate : 2.803 ------------------------------------------------------------------------------- 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 199 SER Chi-restraints excluded: chain A residue 202 ASP 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 B residue 127 PHE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 509 HIS 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 D residue 127 PHE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 202 ASP 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 E residue 20 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 199 SER 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 509 HIS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 87 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 88 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4084 r_free = 0.4084 target = 0.128410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.093444 restraints weight = 131356.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.097396 restraints weight = 55618.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099779 restraints weight = 34954.571| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.6364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16044 Z= 0.158 Angle : 0.541 7.857 21680 Z= 0.294 Chirality : 0.034 0.108 2428 Planarity : 0.003 0.042 2732 Dihedral : 3.968 17.419 2148 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.03 % Allowed : 17.90 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 1936 helix: 1.09 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : 0.15 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 120 HIS 0.003 0.001 HIS B 240 PHE 0.017 0.001 PHE H 93 TYR 0.010 0.001 TYR G 545 ARG 0.009 0.000 ARG B 533 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 1097) hydrogen bonds : angle 4.47961 ( 3243) covalent geometry : bond 0.00323 (16044) covalent geometry : angle 0.54104 (21680) *********************** 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 464 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 414 time to evaluate : 2.405 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: 0.8850 (tp30) cc_final: 0.8292 (mp0) REVERT: A 202 ASP cc_start: 0.9083 (OUTLIER) cc_final: 0.8793 (p0) REVERT: A 301 ASP cc_start: 0.8547 (m-30) cc_final: 0.8332 (m-30) REVERT: A 520 MET cc_start: 0.8881 (ttp) cc_final: 0.8559 (ttp) REVERT: B 202 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8773 (p0) REVERT: B 290 GLU cc_start: 0.8980 (pp20) cc_final: 0.8737 (pp20) REVERT: B 301 ASP cc_start: 0.8525 (m-30) cc_final: 0.8313 (m-30) REVERT: B 520 MET cc_start: 0.8866 (ttp) cc_final: 0.8481 (ttp) REVERT: B 527 LYS cc_start: 0.9618 (tmtt) cc_final: 0.9332 (ttpp) REVERT: B 528 LYS cc_start: 0.9484 (tppt) cc_final: 0.9222 (tppt) REVERT: B 543 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8865 (mt-10) REVERT: C 50 GLN cc_start: 0.9418 (tp40) cc_final: 0.9161 (tm-30) REVERT: C 72 MET cc_start: 0.8501 (tmm) cc_final: 0.7938 (tmm) REVERT: C 73 MET cc_start: 0.8572 (mmm) cc_final: 0.8368 (mmm) REVERT: D 115 GLU cc_start: 0.8859 (tp30) cc_final: 0.8314 (mp0) REVERT: D 202 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8576 (p0) REVERT: D 301 ASP cc_start: 0.8514 (m-30) cc_final: 0.8307 (m-30) REVERT: D 520 MET cc_start: 0.8852 (ttp) cc_final: 0.8368 (ttp) REVERT: D 528 LYS cc_start: 0.9444 (tppt) cc_final: 0.9242 (tppt) REVERT: E 38 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.8889 (ptp-110) REVERT: E 50 GLN cc_start: 0.9412 (tp40) cc_final: 0.9130 (tp-100) REVERT: E 113 LEU cc_start: 0.9128 (mt) cc_final: 0.8628 (tp) REVERT: E 125 MET cc_start: 0.8943 (ttt) cc_final: 0.8652 (ttt) REVERT: F 50 GLN cc_start: 0.9410 (tp40) cc_final: 0.9156 (tm-30) REVERT: F 113 LEU cc_start: 0.9081 (mt) cc_final: 0.8581 (tp) REVERT: F 145 MET cc_start: 0.9119 (ttp) cc_final: 0.8832 (ttp) REVERT: G 301 ASP cc_start: 0.8534 (m-30) cc_final: 0.8330 (m-30) REVERT: G 520 MET cc_start: 0.8856 (ttp) cc_final: 0.8480 (ttp) REVERT: G 527 LYS cc_start: 0.9631 (tmtt) cc_final: 0.9363 (ttpp) REVERT: H 72 MET cc_start: 0.8850 (tmm) cc_final: 0.8500 (tmm) REVERT: H 143 VAL cc_start: 0.9759 (t) cc_final: 0.9546 (p) REVERT: H 144 GLN cc_start: 0.9472 (mm110) cc_final: 0.9246 (mm110) outliers start: 50 outliers final: 36 residues processed: 438 average time/residue: 0.7883 time to fit residues: 470.9389 Evaluate side-chains 413 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 373 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 202 ASP 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 127 PHE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 202 ASP 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 E residue 20 PHE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain G residue 115 GLU 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 509 HIS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 20 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN G 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.126636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.092076 restraints weight = 131427.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.095912 restraints weight = 56279.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098257 restraints weight = 35414.516| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.6706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16044 Z= 0.217 Angle : 0.573 9.125 21680 Z= 0.318 Chirality : 0.035 0.111 2428 Planarity : 0.004 0.049 2732 Dihedral : 4.034 17.484 2148 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.58 % Allowed : 19.42 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 1936 helix: 0.90 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : 0.12 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 176 HIS 0.004 0.001 HIS G 126 PHE 0.020 0.001 PHE H 93 TYR 0.012 0.001 TYR G 545 ARG 0.010 0.001 ARG G 533 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 1097) hydrogen bonds : angle 4.64494 ( 3243) covalent geometry : bond 0.00439 (16044) covalent geometry : angle 0.57290 (21680) *********************** 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 451 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 392 time to evaluate : 2.447 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: A 115 GLU cc_start: 0.8826 (tp30) cc_final: 0.8201 (mp0) REVERT: A 202 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8755 (p0) REVERT: A 520 MET cc_start: 0.8876 (ttp) cc_final: 0.8527 (ttp) REVERT: B 202 ASP cc_start: 0.9110 (OUTLIER) cc_final: 0.8593 (p0) REVERT: B 520 MET cc_start: 0.8862 (ttp) cc_final: 0.8549 (ttp) REVERT: C 50 GLN cc_start: 0.9417 (tp40) cc_final: 0.9126 (tm-30) REVERT: C 52 MET cc_start: 0.8958 (mtt) cc_final: 0.8714 (mtt) REVERT: C 72 MET cc_start: 0.8571 (tmm) cc_final: 0.8126 (tmm) REVERT: C 113 LEU cc_start: 0.9134 (mt) cc_final: 0.8677 (tp) REVERT: D 115 GLU cc_start: 0.8801 (tp30) cc_final: 0.8215 (mp0) REVERT: D 202 ASP cc_start: 0.9050 (OUTLIER) cc_final: 0.8526 (p0) REVERT: D 385 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8823 (pp20) REVERT: D 520 MET cc_start: 0.8815 (ttp) cc_final: 0.8448 (ttp) REVERT: E 50 GLN cc_start: 0.9403 (tp40) cc_final: 0.9162 (tp40) REVERT: F 50 GLN cc_start: 0.9485 (tp40) cc_final: 0.9257 (tm-30) REVERT: F 113 LEU cc_start: 0.9110 (mt) cc_final: 0.8597 (tp) REVERT: F 144 GLN cc_start: 0.9567 (mm110) cc_final: 0.9304 (mm110) REVERT: G 202 ASP cc_start: 0.9070 (OUTLIER) cc_final: 0.8567 (p0) REVERT: H 100 TYR cc_start: 0.9180 (m-80) cc_final: 0.8588 (m-80) outliers start: 59 outliers final: 48 residues processed: 422 average time/residue: 0.8091 time to fit residues: 466.5422 Evaluate side-chains 430 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 378 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 202 ASP 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 514 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 202 ASP 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 E residue 9 GLN Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 183 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.124308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.089480 restraints weight = 133944.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.093235 restraints weight = 57950.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095483 restraints weight = 36800.448| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.6986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 16044 Z= 0.293 Angle : 0.620 6.486 21680 Z= 0.353 Chirality : 0.036 0.207 2428 Planarity : 0.004 0.051 2732 Dihedral : 4.226 18.065 2148 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.25 % Allowed : 19.78 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 1936 helix: 0.65 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.27 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 392 HIS 0.004 0.001 HIS D 126 PHE 0.021 0.002 PHE H 93 TYR 0.013 0.002 TYR G 545 ARG 0.010 0.001 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 1097) hydrogen bonds : angle 4.98037 ( 3243) covalent geometry : bond 0.00585 (16044) covalent geometry : angle 0.61986 (21680) *********************** 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 449 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 379 time to evaluate : 2.681 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: A 115 GLU cc_start: 0.8746 (tp30) cc_final: 0.8135 (mp0) REVERT: A 202 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8814 (p0) REVERT: A 261 GLU cc_start: 0.9286 (mp0) cc_final: 0.9074 (mp0) REVERT: B 385 GLU cc_start: 0.9248 (mm-30) cc_final: 0.9019 (pp20) REVERT: B 520 MET cc_start: 0.8905 (ttp) cc_final: 0.8603 (ttp) REVERT: C 73 MET cc_start: 0.8370 (mmm) cc_final: 0.8127 (mmm) REVERT: D 115 GLU cc_start: 0.8745 (tp30) cc_final: 0.8139 (mp0) REVERT: D 202 ASP cc_start: 0.9097 (OUTLIER) cc_final: 0.8548 (p0) REVERT: D 261 GLU cc_start: 0.9274 (mp0) cc_final: 0.9055 (mp0) REVERT: D 520 MET cc_start: 0.8820 (ttp) cc_final: 0.8459 (ttp) REVERT: F 14 LYS cc_start: 0.9436 (tppt) cc_final: 0.9211 (mttm) REVERT: F 50 GLN cc_start: 0.9460 (tp40) cc_final: 0.9230 (tm-30) REVERT: F 113 LEU cc_start: 0.9128 (mt) cc_final: 0.8603 (tp) REVERT: G 202 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.8583 (p0) REVERT: H 100 TYR cc_start: 0.9033 (m-80) cc_final: 0.8324 (m-80) outliers start: 70 outliers final: 59 residues processed: 419 average time/residue: 0.7969 time to fit residues: 455.9502 Evaluate side-chains 417 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 355 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 202 ASP 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 514 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 171 TYR 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 332 PHE Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 202 ASP 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 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 40 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 284 GLU Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 141 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 HIS D 363 HIS ** 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 = 0.4068 r_free = 0.4068 target = 0.127050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.092381 restraints weight = 131599.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.096273 restraints weight = 56105.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.098703 restraints weight = 35536.986| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.7204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16044 Z= 0.146 Angle : 0.577 8.983 21680 Z= 0.309 Chirality : 0.035 0.116 2428 Planarity : 0.004 0.055 2732 Dihedral : 4.002 16.928 2148 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.61 % Allowed : 23.30 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 1936 helix: 0.96 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : 0.07 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 392 HIS 0.003 0.001 HIS A 240 PHE 0.022 0.001 PHE H 93 TYR 0.012 0.001 TYR G 395 ARG 0.012 0.001 ARG B 533 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 1097) hydrogen bonds : angle 4.46455 ( 3243) covalent geometry : bond 0.00305 (16044) covalent geometry : angle 0.57715 (21680) *********************** 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 453 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 410 time to evaluate : 2.659 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: A 115 GLU cc_start: 0.8741 (tp30) cc_final: 0.8142 (mp0) REVERT: A 130 PHE cc_start: 0.6764 (m-80) cc_final: 0.6550 (m-80) REVERT: A 261 GLU cc_start: 0.9284 (mp0) cc_final: 0.9033 (mp0) REVERT: B 202 ASP cc_start: 0.9091 (p0) cc_final: 0.8853 (p0) REVERT: B 520 MET cc_start: 0.8845 (ttp) cc_final: 0.8548 (ttp) REVERT: B 527 LYS cc_start: 0.9650 (tmtt) cc_final: 0.9353 (ttpp) REVERT: B 543 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8841 (mt-10) REVERT: C 113 LEU cc_start: 0.9184 (mt) cc_final: 0.8713 (tp) REVERT: D 115 GLU cc_start: 0.8745 (tp30) cc_final: 0.8164 (mp0) REVERT: D 130 PHE cc_start: 0.6807 (m-80) cc_final: 0.6602 (m-80) REVERT: D 261 GLU cc_start: 0.9289 (mp0) cc_final: 0.9035 (mp0) REVERT: D 520 MET cc_start: 0.8738 (ttp) cc_final: 0.8435 (ttp) REVERT: E 100 TYR cc_start: 0.9052 (m-80) cc_final: 0.8569 (m-80) REVERT: E 113 LEU cc_start: 0.9147 (mt) cc_final: 0.8664 (tp) REVERT: F 50 GLN cc_start: 0.9441 (tp40) cc_final: 0.9202 (tm-30) REVERT: F 113 LEU cc_start: 0.9092 (mt) cc_final: 0.8665 (tp) REVERT: G 202 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8535 (p0) REVERT: H 100 TYR cc_start: 0.9052 (m-80) cc_final: 0.8440 (m-80) outliers start: 43 outliers final: 34 residues processed: 433 average time/residue: 0.7907 time to fit residues: 472.5844 Evaluate side-chains 411 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 376 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET 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 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 332 PHE Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 101 ILE 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 E residue 40 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 202 ASP 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 357 GLN Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 164 optimal weight: 0.6980 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 363 HIS ** 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 = 0.4051 r_free = 0.4051 target = 0.125889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.091095 restraints weight = 132780.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.095073 restraints weight = 56367.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.097456 restraints weight = 35267.289| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.7401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16044 Z= 0.196 Angle : 0.593 7.793 21680 Z= 0.326 Chirality : 0.035 0.138 2428 Planarity : 0.004 0.065 2732 Dihedral : 4.059 17.334 2148 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.03 % Allowed : 23.79 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1936 helix: 0.84 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : 0.10 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 392 HIS 0.003 0.001 HIS G 258 PHE 0.025 0.001 PHE H 93 TYR 0.017 0.001 TYR B 395 ARG 0.013 0.001 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 1097) hydrogen bonds : angle 4.60588 ( 3243) covalent geometry : bond 0.00405 (16044) covalent geometry : angle 0.59301 (21680) *********************** 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 436 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 386 time to evaluate : 2.705 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: A 115 GLU cc_start: 0.8704 (tp30) cc_final: 0.8056 (mp0) REVERT: A 130 PHE cc_start: 0.6896 (m-80) cc_final: 0.6672 (m-80) REVERT: B 130 PHE cc_start: 0.6904 (m-80) cc_final: 0.6575 (m-10) REVERT: B 202 ASP cc_start: 0.9069 (p0) cc_final: 0.8824 (p0) REVERT: B 520 MET cc_start: 0.8801 (ttp) cc_final: 0.8512 (ttp) REVERT: B 527 LYS cc_start: 0.9630 (tmtt) cc_final: 0.9372 (ttpp) REVERT: C 113 LEU cc_start: 0.9165 (mt) cc_final: 0.8691 (tp) REVERT: D 115 GLU cc_start: 0.8645 (tp30) cc_final: 0.8082 (mp0) REVERT: D 130 PHE cc_start: 0.6882 (m-80) cc_final: 0.6655 (m-80) REVERT: D 559 LEU cc_start: 0.8207 (mt) cc_final: 0.7861 (tt) REVERT: E 100 TYR cc_start: 0.9082 (m-80) cc_final: 0.8635 (m-80) REVERT: F 50 GLN cc_start: 0.9427 (tp40) cc_final: 0.9188 (tm-30) REVERT: F 87 ARG cc_start: 0.9005 (mtt90) cc_final: 0.8679 (ttm170) REVERT: F 113 LEU cc_start: 0.9062 (mt) cc_final: 0.8638 (tp) REVERT: G 130 PHE cc_start: 0.6903 (m-80) cc_final: 0.6572 (m-10) REVERT: G 202 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8789 (p0) REVERT: G 242 ASP cc_start: 0.6204 (t0) cc_final: 0.5709 (p0) outliers start: 50 outliers final: 42 residues processed: 413 average time/residue: 0.7953 time to fit residues: 449.3879 Evaluate side-chains 421 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 378 time to evaluate : 2.611 ------------------------------------------------------------------------------- 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 159 MET Chi-restraints excluded: chain A residue 162 VAL 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 388 ASP Chi-restraints excluded: chain A residue 509 HIS 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 332 PHE Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 101 ILE 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 340 PHE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 284 GLU Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 175 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.126766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.091744 restraints weight = 132044.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095785 restraints weight = 56103.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.098187 restraints weight = 35180.946| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.7522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16044 Z= 0.157 Angle : 0.586 7.137 21680 Z= 0.315 Chirality : 0.035 0.135 2428 Planarity : 0.004 0.068 2732 Dihedral : 3.962 18.152 2148 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.79 % Allowed : 24.45 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.19), residues: 1936 helix: 1.00 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : 0.19 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 392 HIS 0.004 0.001 HIS G 240 PHE 0.025 0.001 PHE H 93 TYR 0.016 0.001 TYR D 395 ARG 0.013 0.001 ARG B 533 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 1097) hydrogen bonds : angle 4.43792 ( 3243) covalent geometry : bond 0.00329 (16044) covalent geometry : angle 0.58623 (21680) ********************** 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 449 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 403 time to evaluate : 2.869 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: 0.8723 (tp30) cc_final: 0.7920 (mp0) REVERT: A 130 PHE cc_start: 0.6807 (m-80) cc_final: 0.6578 (m-80) REVERT: A 537 ASP cc_start: 0.9416 (t0) cc_final: 0.9093 (t0) REVERT: B 130 PHE cc_start: 0.6938 (m-80) cc_final: 0.6656 (m-80) REVERT: B 202 ASP cc_start: 0.9000 (p0) cc_final: 0.8673 (p0) REVERT: B 242 ASP cc_start: 0.6203 (t0) cc_final: 0.5915 (p0) REVERT: B 527 LYS cc_start: 0.9626 (tmtt) cc_final: 0.9370 (ttpp) REVERT: B 543 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8821 (mt-10) REVERT: C 113 LEU cc_start: 0.9189 (mt) cc_final: 0.8731 (tp) REVERT: D 115 GLU cc_start: 0.8687 (tp30) cc_final: 0.8112 (mp0) REVERT: D 130 PHE cc_start: 0.6866 (m-80) cc_final: 0.6567 (m-80) REVERT: E 100 TYR cc_start: 0.9087 (m-80) cc_final: 0.8671 (m-80) REVERT: F 50 GLN cc_start: 0.9429 (tp40) cc_final: 0.9189 (tm-30) REVERT: F 87 ARG cc_start: 0.9024 (mtt90) cc_final: 0.8699 (ttm170) REVERT: G 130 PHE cc_start: 0.6979 (m-80) cc_final: 0.6733 (m-80) REVERT: G 202 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8738 (p0) REVERT: H 88 GLU cc_start: 0.9064 (tp30) cc_final: 0.8864 (tp30) outliers start: 46 outliers final: 40 residues processed: 427 average time/residue: 0.7813 time to fit residues: 456.7063 Evaluate side-chains 429 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 388 time to evaluate : 2.591 ------------------------------------------------------------------------------- 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 159 MET Chi-restraints excluded: chain A residue 171 TYR 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 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 273 LEU Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 20 PHE 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 388 ASP Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 202 ASP 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 357 GLN Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 26 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 HIS B 240 HIS B 363 HIS ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.127598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.093038 restraints weight = 129279.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.096930 restraints weight = 55529.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.099386 restraints weight = 34942.893| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.7602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16044 Z= 0.142 Angle : 0.590 7.530 21680 Z= 0.316 Chirality : 0.035 0.134 2428 Planarity : 0.004 0.066 2732 Dihedral : 3.898 18.910 2148 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.49 % Allowed : 24.82 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.19), residues: 1936 helix: 1.21 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : 0.19 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 392 HIS 0.003 0.001 HIS A 240 PHE 0.024 0.001 PHE H 93 TYR 0.026 0.001 TYR D 545 ARG 0.013 0.001 ARG B 533 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 1097) hydrogen bonds : angle 4.36177 ( 3243) covalent geometry : bond 0.00301 (16044) covalent geometry : angle 0.58987 (21680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13144.20 seconds wall clock time: 226 minutes 27.28 seconds (13587.28 seconds total)