Starting phenix.real_space_refine on Thu Mar 21 23:47:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xni_33316/03_2024/7xni_33316_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xni_33316/03_2024/7xni_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xni_33316/03_2024/7xni_33316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xni_33316/03_2024/7xni_33316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xni_33316/03_2024/7xni_33316_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xni_33316/03_2024/7xni_33316_neut.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 13.22, per 1000 atoms: 0.42 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 - 3.50 Amino acid : False - 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: 25.04 Conformation dependent library (CDL) restraints added in 3.0 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: 2.19 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: 11.00 Time building geometry restraints manager: 26.05 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: 97.62 - 104.99: 276 104.99 - 112.36: 35440 112.36 - 119.73: 9131 119.73 - 127.10: 12041 127.10 - 134.47: 184 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 1.850 nonbonded pdb=" H ASN B 289 " pdb=" O ARG B 293 " model vdw 1.537 1.850 nonbonded pdb=" H ASN A 289 " pdb=" O ARG A 293 " model vdw 1.537 1.850 nonbonded pdb=" H ASN D 289 " pdb=" O ARG D 293 " model vdw 1.537 1.850 nonbonded pdb=" O ARG D 360 " pdb=" HD1 HIS D 363 " model vdw 1.595 1.850 ... (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 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: 0.880 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: 0.460 Extract box with map and model: 4.700 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 93.000 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 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:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.640 ------------------------------------------------------------------------------- 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= 0.757 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 619 time to evaluate : 2.439 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: 0.8513 time to fit residues: 698.1905 Evaluate side-chains 402 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 2.396 ------------------------------------------------------------------------------- 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: 2.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 521 GLN B 544 GLN ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN ** D 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 H 112 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16044 Z= 0.196 Angle : 0.581 6.788 21680 Z= 0.319 Chirality : 0.035 0.122 2428 Planarity : 0.004 0.061 2732 Dihedral : 4.631 20.305 2148 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.70 % Allowed : 12.01 % Favored : 86.29 % 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: -1.34 (0.17), residues: 1936 helix: -0.72 (0.12), residues: 1460 sheet: None (None), residues: 0 loop : -0.87 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 120 HIS 0.004 0.001 HIS C 108 PHE 0.019 0.002 PHE H 69 TYR 0.023 0.001 TYR G 545 ARG 0.004 0.001 ARG A 555 *********************** 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 522 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 494 time to evaluate : 2.428 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: A 123 PHE cc_start: 0.8377 (t80) cc_final: 0.8123 (t80) REVERT: A 210 MET cc_start: 0.8287 (mmt) cc_final: 0.7779 (tmm) REVERT: A 520 MET cc_start: 0.8878 (ttp) cc_final: 0.8450 (ttp) REVERT: A 540 ASP cc_start: 0.9219 (m-30) cc_final: 0.8967 (m-30) REVERT: B 123 PHE cc_start: 0.8335 (t80) cc_final: 0.8098 (t80) REVERT: B 210 MET cc_start: 0.8283 (mmt) cc_final: 0.7762 (tmm) REVERT: B 520 MET cc_start: 0.8977 (ttp) cc_final: 0.8536 (ttp) REVERT: C 50 GLN cc_start: 0.9370 (tp40) cc_final: 0.9006 (tm-30) REVERT: C 72 MET cc_start: 0.8698 (tmm) cc_final: 0.8253 (tmm) REVERT: C 110 MET cc_start: 0.9413 (mmp) cc_final: 0.9126 (mmp) REVERT: C 126 ILE cc_start: 0.9311 (mm) cc_final: 0.9056 (tt) REVERT: C 145 MET cc_start: 0.9194 (ttp) cc_final: 0.8953 (ttp) REVERT: D 123 PHE cc_start: 0.8397 (t80) cc_final: 0.8147 (t80) REVERT: D 210 MET cc_start: 0.8285 (mmt) cc_final: 0.7781 (tmm) REVERT: D 544 GLN cc_start: 0.8741 (pp30) cc_final: 0.8508 (pp30) REVERT: E 49 LEU cc_start: 0.8978 (mt) cc_final: 0.8614 (mt) REVERT: E 50 GLN cc_start: 0.9413 (tp40) cc_final: 0.9187 (tp40) REVERT: E 75 ARG cc_start: 0.8170 (ptp90) cc_final: 0.7703 (ptt90) REVERT: E 119 ASP cc_start: 0.8589 (t0) cc_final: 0.8373 (t0) REVERT: E 123 ASP cc_start: 0.8461 (m-30) cc_final: 0.8176 (m-30) REVERT: F 14 LYS cc_start: 0.9373 (tppt) cc_final: 0.9133 (mttp) REVERT: F 50 GLN cc_start: 0.9408 (tp40) cc_final: 0.9137 (tm-30) REVERT: F 110 MET cc_start: 0.9414 (mmp) cc_final: 0.9127 (mmp) REVERT: F 119 ASP cc_start: 0.8662 (t0) cc_final: 0.8410 (t0) REVERT: G 210 MET cc_start: 0.8307 (mmt) cc_final: 0.7793 (tmm) REVERT: G 284 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7911 (mm-30) REVERT: G 520 MET cc_start: 0.8967 (ttp) cc_final: 0.8444 (ttp) REVERT: H 29 THR cc_start: 0.8871 (m) cc_final: 0.8634 (p) REVERT: H 49 LEU cc_start: 0.9083 (mt) cc_final: 0.8723 (mt) REVERT: H 72 MET cc_start: 0.8820 (tmm) cc_final: 0.8473 (tmm) REVERT: H 119 ASP cc_start: 0.9071 (t0) cc_final: 0.8346 (t0) REVERT: H 123 ASP cc_start: 0.9440 (t0) cc_final: 0.9158 (m-30) outliers start: 28 outliers final: 23 residues processed: 507 average time/residue: 0.8095 time to fit residues: 555.1175 Evaluate side-chains 438 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 415 time to evaluate : 2.430 ------------------------------------------------------------------------------- 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 276 SER Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 138 ASN 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 F residue 138 ASN 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 96 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16044 Z= 0.291 Angle : 0.593 6.713 21680 Z= 0.332 Chirality : 0.035 0.106 2428 Planarity : 0.004 0.042 2732 Dihedral : 4.387 18.611 2148 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.58 % Allowed : 14.68 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.05 (0.18), residues: 1936 helix: 0.27 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.63 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 120 HIS 0.003 0.001 HIS A 126 PHE 0.018 0.002 PHE H 69 TYR 0.013 0.002 TYR G 545 ARG 0.009 0.001 ARG G 533 *********************** 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 483 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 424 time to evaluate : 2.474 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: A 202 ASP cc_start: 0.9104 (OUTLIER) cc_final: 0.8518 (p0) REVERT: A 210 MET cc_start: 0.8259 (mmt) cc_final: 0.7676 (tmm) REVERT: B 124 VAL cc_start: 0.8348 (t) cc_final: 0.8085 (p) REVERT: B 238 MET cc_start: 0.6059 (mmt) cc_final: 0.5859 (mmt) REVERT: B 520 MET cc_start: 0.8971 (ttp) cc_final: 0.8540 (ttp) REVERT: C 50 GLN cc_start: 0.9417 (tp40) cc_final: 0.9058 (tm-30) REVERT: C 72 MET cc_start: 0.8821 (tmm) cc_final: 0.8344 (tmm) REVERT: C 73 MET cc_start: 0.8697 (mmm) cc_final: 0.8446 (mmm) REVERT: D 202 ASP cc_start: 0.9117 (OUTLIER) cc_final: 0.8538 (p0) REVERT: D 210 MET cc_start: 0.8254 (mmt) cc_final: 0.7669 (tmm) REVERT: E 38 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.9127 (ptp-110) REVERT: E 50 GLN cc_start: 0.9385 (tp40) cc_final: 0.9173 (tp40) REVERT: E 73 MET cc_start: 0.8674 (mmm) cc_final: 0.8442 (mmm) REVERT: E 110 MET cc_start: 0.9508 (mmp) cc_final: 0.9027 (mmp) REVERT: E 125 MET cc_start: 0.8925 (ttt) cc_final: 0.8576 (ttt) REVERT: F 38 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.8975 (ptp-110) REVERT: F 50 GLN cc_start: 0.9331 (tp40) cc_final: 0.9127 (tm-30) REVERT: G 202 ASP cc_start: 0.9139 (OUTLIER) cc_final: 0.8556 (p0) REVERT: G 520 MET cc_start: 0.8920 (ttp) cc_final: 0.8449 (ttp) REVERT: G 540 ASP cc_start: 0.9094 (OUTLIER) cc_final: 0.8818 (m-30) REVERT: H 73 MET cc_start: 0.8752 (mmm) cc_final: 0.8477 (mmm) REVERT: H 75 ARG cc_start: 0.8116 (ptp90) cc_final: 0.7719 (ptt90) REVERT: H 87 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8329 (mtt90) REVERT: H 100 TYR cc_start: 0.8965 (m-80) cc_final: 0.8263 (m-80) REVERT: H 113 LEU cc_start: 0.9177 (mt) cc_final: 0.8666 (tp) REVERT: H 119 ASP cc_start: 0.9078 (t0) cc_final: 0.8370 (t0) REVERT: H 123 ASP cc_start: 0.9448 (t0) cc_final: 0.9149 (m-30) outliers start: 59 outliers final: 46 residues processed: 462 average time/residue: 0.8209 time to fit residues: 525.2831 Evaluate side-chains 439 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 386 time to evaluate : 2.529 ------------------------------------------------------------------------------- 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 332 PHE Chi-restraints excluded: chain A residue 340 PHE 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 125 TYR 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 276 SER 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 514 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain D residue 110 VAL 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 E residue 20 PHE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain G residue 125 TYR Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 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 540 ASP Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 138 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 91 optimal weight: 0.4980 chunk 166 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16044 Z= 0.213 Angle : 0.540 7.628 21680 Z= 0.296 Chirality : 0.034 0.120 2428 Planarity : 0.003 0.042 2732 Dihedral : 4.063 18.612 2148 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.40 % Allowed : 16.63 % Favored : 79.98 % 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: 0.93 (0.19), residues: 1936 helix: 0.99 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.32 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 120 HIS 0.002 0.001 HIS F 108 PHE 0.018 0.001 PHE H 69 TYR 0.011 0.001 TYR B 545 ARG 0.009 0.001 ARG B 533 *********************** 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 494 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 438 time to evaluate : 2.742 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: A 202 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8767 (p0) REVERT: A 520 MET cc_start: 0.8917 (ttp) cc_final: 0.8540 (ttp) REVERT: B 202 ASP cc_start: 0.9151 (OUTLIER) cc_final: 0.8688 (p0) REVERT: B 238 MET cc_start: 0.5931 (mmt) cc_final: 0.5700 (mmt) REVERT: B 520 MET cc_start: 0.8942 (ttp) cc_final: 0.8485 (ttp) REVERT: C 50 GLN cc_start: 0.9395 (tp40) cc_final: 0.9073 (tm-30) REVERT: C 72 MET cc_start: 0.8754 (tmm) cc_final: 0.7860 (tmm) REVERT: C 87 ARG cc_start: 0.8894 (ttm110) cc_final: 0.8686 (mtt90) REVERT: C 113 LEU cc_start: 0.9029 (mt) cc_final: 0.8470 (tp) REVERT: D 202 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8767 (p0) REVERT: E 50 GLN cc_start: 0.9375 (tp40) cc_final: 0.9127 (tp40) REVERT: E 73 MET cc_start: 0.8639 (mmm) cc_final: 0.8415 (mmm) REVERT: E 125 MET cc_start: 0.8974 (ttt) cc_final: 0.8713 (ttt) REVERT: F 50 GLN cc_start: 0.9325 (tp40) cc_final: 0.9123 (tm-30) REVERT: F 144 GLN cc_start: 0.9551 (mm110) cc_final: 0.9307 (mm110) REVERT: G 202 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8535 (p0) REVERT: G 520 MET cc_start: 0.8876 (ttp) cc_final: 0.8450 (ttp) REVERT: H 75 ARG cc_start: 0.8071 (ptp90) cc_final: 0.7514 (ptt90) REVERT: H 87 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8424 (mtt90) REVERT: H 113 LEU cc_start: 0.9164 (mt) cc_final: 0.8712 (tp) REVERT: H 119 ASP cc_start: 0.9112 (t0) cc_final: 0.8412 (t0) REVERT: H 123 ASP cc_start: 0.9314 (t0) cc_final: 0.9072 (m-30) outliers start: 56 outliers final: 42 residues processed: 461 average time/residue: 0.7887 time to fit residues: 505.6811 Evaluate side-chains 438 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 391 time to evaluate : 2.855 ------------------------------------------------------------------------------- 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 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 509 HIS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 115 GLU 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 276 SER 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 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 264 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain E residue 20 PHE 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 F residue 51 ASP Chi-restraints excluded: chain F residue 126 ILE 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 202 ASP 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 Chi-restraints excluded: chain H residue 51 ASP 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 154 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 166 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 363 HIS ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.6365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16044 Z= 0.236 Angle : 0.555 8.097 21680 Z= 0.304 Chirality : 0.034 0.105 2428 Planarity : 0.003 0.041 2732 Dihedral : 4.020 18.019 2148 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.58 % Allowed : 18.26 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.12 (0.19), residues: 1936 helix: 1.10 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.15 (0.30), residues: 464 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 0.019 0.001 PHE H 93 TYR 0.010 0.001 TYR B 545 ARG 0.009 0.000 ARG D 533 *********************** 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 470 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 411 time to evaluate : 2.270 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: A 115 GLU cc_start: 0.8860 (tp30) cc_final: 0.8304 (mp0) REVERT: A 202 ASP cc_start: 0.9081 (OUTLIER) cc_final: 0.8798 (p0) REVERT: A 520 MET cc_start: 0.8876 (ttp) cc_final: 0.8558 (ttp) REVERT: B 202 ASP cc_start: 0.9167 (p0) cc_final: 0.8711 (p0) REVERT: B 238 MET cc_start: 0.5940 (mmt) cc_final: 0.5667 (mmt) REVERT: B 520 MET cc_start: 0.8916 (ttp) cc_final: 0.8509 (ttp) REVERT: C 50 GLN cc_start: 0.9400 (tp40) cc_final: 0.9138 (tm-30) REVERT: C 113 LEU cc_start: 0.9038 (mt) cc_final: 0.8494 (tp) REVERT: D 115 GLU cc_start: 0.8856 (tp30) cc_final: 0.8295 (mp0) REVERT: D 202 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8796 (p0) REVERT: E 50 GLN cc_start: 0.9355 (tp40) cc_final: 0.9099 (tp40) REVERT: E 73 MET cc_start: 0.8694 (mmm) cc_final: 0.8483 (mmm) REVERT: E 125 MET cc_start: 0.9032 (ttt) cc_final: 0.8779 (ttt) REVERT: F 50 GLN cc_start: 0.9326 (tp40) cc_final: 0.9091 (tm-30) REVERT: F 87 ARG cc_start: 0.8974 (mtt90) cc_final: 0.8699 (ttm170) REVERT: G 202 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8807 (p0) REVERT: G 520 MET cc_start: 0.8871 (ttp) cc_final: 0.8493 (ttp) REVERT: H 75 ARG cc_start: 0.8100 (ptp90) cc_final: 0.7645 (ptt90) REVERT: H 87 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8558 (mtt90) REVERT: H 113 LEU cc_start: 0.9183 (mt) cc_final: 0.8727 (tp) REVERT: H 119 ASP cc_start: 0.9103 (t0) cc_final: 0.8391 (t0) REVERT: H 123 ASP cc_start: 0.9302 (t0) cc_final: 0.9030 (m-30) outliers start: 59 outliers final: 48 residues processed: 438 average time/residue: 0.7913 time to fit residues: 475.6236 Evaluate side-chains 445 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 393 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 540 ASP 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 264 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 SER 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 514 ILE Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 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 D residue 540 ASP Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain G residue 115 GLU 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 276 SER Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 381 CYS Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 87 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 6.9990 chunk 167 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN B 234 GLN D 234 GLN ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.6690 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= 0.231 Angle : 0.550 7.443 21680 Z= 0.302 Chirality : 0.034 0.106 2428 Planarity : 0.003 0.044 2732 Dihedral : 3.969 17.374 2148 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.28 % Allowed : 20.39 % Favored : 76.33 % 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: 1.06 (0.19), residues: 1936 helix: 1.07 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -0.29 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 176 HIS 0.003 0.001 HIS B 126 PHE 0.019 0.001 PHE H 93 TYR 0.010 0.001 TYR A 545 ARG 0.010 0.001 ARG B 533 *********************** 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 467 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 413 time to evaluate : 2.349 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: A 115 GLU cc_start: 0.8812 (tp30) cc_final: 0.8260 (mp0) REVERT: A 202 ASP cc_start: 0.9071 (OUTLIER) cc_final: 0.8830 (p0) REVERT: A 520 MET cc_start: 0.8848 (ttp) cc_final: 0.8543 (ttp) REVERT: A 537 ASP cc_start: 0.9314 (t0) cc_final: 0.9051 (t0) REVERT: B 238 MET cc_start: 0.5921 (mmt) cc_final: 0.5557 (mmt) REVERT: B 520 MET cc_start: 0.8890 (ttp) cc_final: 0.8512 (ttp) REVERT: B 527 LYS cc_start: 0.9596 (tmtt) cc_final: 0.9321 (ttpp) REVERT: C 50 GLN cc_start: 0.9393 (tp40) cc_final: 0.9056 (tm-30) REVERT: C 87 ARG cc_start: 0.8950 (ttm110) cc_final: 0.8543 (mtt90) REVERT: C 113 LEU cc_start: 0.9018 (mt) cc_final: 0.8553 (tp) REVERT: D 115 GLU cc_start: 0.8807 (tp30) cc_final: 0.8226 (mp0) REVERT: E 50 GLN cc_start: 0.9356 (tp40) cc_final: 0.9092 (tp40) REVERT: E 113 LEU cc_start: 0.9021 (mt) cc_final: 0.8472 (tp) REVERT: F 9 GLN cc_start: 0.5823 (OUTLIER) cc_final: 0.5604 (pt0) REVERT: F 50 GLN cc_start: 0.9371 (tp40) cc_final: 0.9095 (tm-30) REVERT: F 87 ARG cc_start: 0.9034 (mtt90) cc_final: 0.8808 (mtt90) REVERT: G 202 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8767 (p0) REVERT: H 87 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8327 (mtt90) REVERT: H 100 TYR cc_start: 0.9063 (m-80) cc_final: 0.8472 (m-80) outliers start: 54 outliers final: 45 residues processed: 438 average time/residue: 0.7662 time to fit residues: 456.6010 Evaluate side-chains 435 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 386 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 540 ASP Chi-restraints excluded: chain A residue 552 LEU 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 276 SER Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 540 ASP 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 264 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 51 ASP 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 276 SER Chi-restraints excluded: chain G residue 284 GLU Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 381 CYS Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 87 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 185 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 HIS D 363 HIS ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16044 Z= 0.165 Angle : 0.547 7.588 21680 Z= 0.289 Chirality : 0.034 0.127 2428 Planarity : 0.003 0.047 2732 Dihedral : 3.859 17.247 2148 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.67 % Allowed : 22.57 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.54 (0.19), residues: 1936 helix: 1.37 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.01 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 120 HIS 0.003 0.001 HIS A 240 PHE 0.021 0.001 PHE H 93 TYR 0.009 0.001 TYR A 545 ARG 0.011 0.000 ARG A 533 *********************** 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 476 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 432 time to evaluate : 2.425 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: A 115 GLU cc_start: 0.8783 (tp30) cc_final: 0.8229 (mp0) REVERT: A 130 PHE cc_start: 0.6864 (m-80) cc_final: 0.6568 (m-80) REVERT: A 537 ASP cc_start: 0.9325 (t0) cc_final: 0.9062 (t0) REVERT: B 202 ASP cc_start: 0.9142 (OUTLIER) cc_final: 0.8559 (p0) REVERT: B 238 MET cc_start: 0.5765 (mmt) cc_final: 0.5279 (mmt) REVERT: B 520 MET cc_start: 0.8860 (ttp) cc_final: 0.8499 (ttp) REVERT: B 527 LYS cc_start: 0.9577 (tmtt) cc_final: 0.9312 (ttpp) REVERT: C 113 LEU cc_start: 0.9062 (mt) cc_final: 0.8603 (tp) REVERT: D 115 GLU cc_start: 0.8826 (tp30) cc_final: 0.8207 (mp0) REVERT: D 130 PHE cc_start: 0.6840 (m-80) cc_final: 0.6639 (m-80) REVERT: D 537 ASP cc_start: 0.9309 (t0) cc_final: 0.9027 (t0) REVERT: E 50 GLN cc_start: 0.9361 (tp40) cc_final: 0.9032 (tp40) REVERT: E 54 ASN cc_start: 0.9351 (p0) cc_final: 0.9145 (p0) REVERT: E 113 LEU cc_start: 0.9058 (mt) cc_final: 0.8530 (tp) REVERT: F 50 GLN cc_start: 0.9429 (tp40) cc_final: 0.9134 (tm-30) REVERT: F 87 ARG cc_start: 0.8972 (mtt90) cc_final: 0.8702 (mmt90) REVERT: F 113 LEU cc_start: 0.8891 (mt) cc_final: 0.8370 (tp) REVERT: H 91 ARG cc_start: 0.8768 (mtt180) cc_final: 0.8431 (mtt90) outliers start: 44 outliers final: 34 residues processed: 455 average time/residue: 0.7706 time to fit residues: 475.7285 Evaluate side-chains 431 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 396 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 552 LEU 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 276 SER Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 388 ASP 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 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 70 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 20 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 GLN ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.7112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16044 Z= 0.260 Angle : 0.580 7.933 21680 Z= 0.319 Chirality : 0.034 0.105 2428 Planarity : 0.004 0.060 2732 Dihedral : 3.970 17.791 2148 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.64 % Allowed : 22.33 % Favored : 74.03 % 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: 1.32 (0.19), residues: 1936 helix: 1.22 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -0.11 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 379 HIS 0.003 0.001 HIS B 240 PHE 0.023 0.002 PHE H 93 TYR 0.012 0.001 TYR D 395 ARG 0.012 0.001 ARG B 533 *********************** 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 458 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 398 time to evaluate : 2.285 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: A 115 GLU cc_start: 0.8759 (tp30) cc_final: 0.8128 (mp0) REVERT: A 130 PHE cc_start: 0.6842 (m-80) cc_final: 0.6619 (m-80) REVERT: A 537 ASP cc_start: 0.9342 (t0) cc_final: 0.9089 (t0) REVERT: B 130 PHE cc_start: 0.6906 (m-80) cc_final: 0.6596 (m-10) REVERT: B 238 MET cc_start: 0.5640 (mmt) cc_final: 0.5176 (mmt) REVERT: B 240 HIS cc_start: 0.8132 (m170) cc_final: 0.7867 (m170) REVERT: B 242 ASP cc_start: 0.6167 (t0) cc_final: 0.5608 (p0) REVERT: B 520 MET cc_start: 0.8841 (ttp) cc_final: 0.8503 (ttp) REVERT: B 527 LYS cc_start: 0.9592 (tmtt) cc_final: 0.9348 (ttpp) REVERT: C 87 ARG cc_start: 0.8819 (ttm110) cc_final: 0.8581 (mtt90) REVERT: D 115 GLU cc_start: 0.8767 (tp30) cc_final: 0.8118 (mp0) REVERT: D 130 PHE cc_start: 0.6833 (m-80) cc_final: 0.6613 (m-80) REVERT: D 537 ASP cc_start: 0.9333 (t0) cc_final: 0.9056 (t0) REVERT: E 50 GLN cc_start: 0.9343 (tp40) cc_final: 0.8983 (tp40) REVERT: E 113 LEU cc_start: 0.9012 (mt) cc_final: 0.8469 (tp) REVERT: F 50 GLN cc_start: 0.9413 (tp40) cc_final: 0.9152 (tm-30) REVERT: F 87 ARG cc_start: 0.9044 (mtt90) cc_final: 0.8768 (mmt90) REVERT: G 130 PHE cc_start: 0.6820 (m-80) cc_final: 0.6595 (m-80) REVERT: G 242 ASP cc_start: 0.6017 (t0) cc_final: 0.5505 (p0) REVERT: H 91 ARG cc_start: 0.8851 (mtt180) cc_final: 0.8539 (mtt90) REVERT: H 100 TYR cc_start: 0.9001 (m-80) cc_final: 0.8315 (m-80) REVERT: H 119 ASP cc_start: 0.9095 (t0) cc_final: 0.8383 (t0) REVERT: H 123 ASP cc_start: 0.9525 (t0) cc_final: 0.9027 (m-30) REVERT: H 144 GLN cc_start: 0.9494 (mm110) cc_final: 0.9128 (mm110) outliers start: 60 outliers final: 55 residues processed: 424 average time/residue: 0.7626 time to fit residues: 441.0932 Evaluate side-chains 441 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 386 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 171 TYR 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 276 SER Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 559 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 264 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 388 ASP Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 540 ASP Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 20 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 HIS ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.7256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16044 Z= 0.200 Angle : 0.576 7.715 21680 Z= 0.309 Chirality : 0.034 0.107 2428 Planarity : 0.004 0.121 2732 Dihedral : 3.880 18.634 2148 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.97 % Allowed : 23.42 % Favored : 73.60 % 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: 1.50 (0.19), residues: 1936 helix: 1.34 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -0.02 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 379 HIS 0.003 0.001 HIS B 240 PHE 0.023 0.001 PHE E 93 TYR 0.015 0.001 TYR G 395 ARG 0.017 0.001 ARG G 533 *********************** 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 456 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 407 time to evaluate : 2.560 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: A 115 GLU cc_start: 0.8766 (tp30) cc_final: 0.8120 (mp0) REVERT: A 130 PHE cc_start: 0.6840 (m-80) cc_final: 0.6622 (m-80) REVERT: A 537 ASP cc_start: 0.9344 (t0) cc_final: 0.9084 (t0) REVERT: B 130 PHE cc_start: 0.6956 (m-80) cc_final: 0.6720 (m-80) REVERT: B 202 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8548 (p0) REVERT: B 238 MET cc_start: 0.5636 (mmt) cc_final: 0.5179 (mmt) REVERT: B 527 LYS cc_start: 0.9584 (tmtt) cc_final: 0.9302 (ttpp) REVERT: B 537 ASP cc_start: 0.9305 (t0) cc_final: 0.9048 (t0) REVERT: D 115 GLU cc_start: 0.8758 (tp30) cc_final: 0.8123 (mp0) REVERT: D 130 PHE cc_start: 0.6837 (m-80) cc_final: 0.6616 (m-80) REVERT: D 537 ASP cc_start: 0.9345 (t0) cc_final: 0.9070 (t0) REVERT: E 50 GLN cc_start: 0.9326 (tp40) cc_final: 0.9004 (tp-100) REVERT: E 91 ARG cc_start: 0.8845 (mtt180) cc_final: 0.8502 (mtt90) REVERT: E 113 LEU cc_start: 0.9003 (mt) cc_final: 0.8471 (tp) REVERT: F 50 GLN cc_start: 0.9397 (tp40) cc_final: 0.9089 (tm-30) REVERT: F 87 ARG cc_start: 0.9020 (mtt90) cc_final: 0.8811 (mmt90) REVERT: G 130 PHE cc_start: 0.6836 (m-80) cc_final: 0.6584 (m-80) REVERT: H 91 ARG cc_start: 0.8841 (mtt180) cc_final: 0.8511 (mtt90) REVERT: H 100 TYR cc_start: 0.9041 (m-80) cc_final: 0.8468 (m-80) REVERT: H 144 GLN cc_start: 0.9491 (mm110) cc_final: 0.9111 (mm110) outliers start: 49 outliers final: 47 residues processed: 428 average time/residue: 0.8134 time to fit residues: 482.9875 Evaluate side-chains 440 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 392 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 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 547 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 559 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 276 SER Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 540 ASP 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 264 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 381 CYS Chi-restraints excluded: chain G residue 388 ASP Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 540 ASP Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain H residue 20 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 191 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 152 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 HIS G 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16044 Z= 0.202 Angle : 0.586 9.113 21680 Z= 0.314 Chirality : 0.034 0.111 2428 Planarity : 0.004 0.118 2732 Dihedral : 3.857 19.960 2148 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.22 % Allowed : 23.30 % Favored : 73.48 % 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: 1.56 (0.19), residues: 1936 helix: 1.38 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : 0.01 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 379 HIS 0.003 0.001 HIS B 240 PHE 0.024 0.001 PHE E 93 TYR 0.019 0.001 TYR A 267 ARG 0.018 0.001 ARG A 533 ********************** 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 456 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 403 time to evaluate : 2.442 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: A 115 GLU cc_start: 0.8757 (tp30) cc_final: 0.8092 (mp0) REVERT: A 130 PHE cc_start: 0.6801 (m-80) cc_final: 0.6575 (m-80) REVERT: A 537 ASP cc_start: 0.9296 (t0) cc_final: 0.9036 (t0) REVERT: B 130 PHE cc_start: 0.6936 (m-80) cc_final: 0.6701 (m-80) REVERT: B 202 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.8496 (p0) REVERT: B 527 LYS cc_start: 0.9587 (tmtt) cc_final: 0.9284 (ttpp) REVERT: B 537 ASP cc_start: 0.9290 (t0) cc_final: 0.9025 (t0) REVERT: C 145 MET cc_start: 0.8943 (ttp) cc_final: 0.8740 (ttp) REVERT: D 115 GLU cc_start: 0.8762 (tp30) cc_final: 0.8103 (mp0) REVERT: D 130 PHE cc_start: 0.6892 (m-80) cc_final: 0.6635 (m-80) REVERT: D 537 ASP cc_start: 0.9356 (t0) cc_final: 0.9083 (t0) REVERT: E 50 GLN cc_start: 0.9319 (tp40) cc_final: 0.8998 (tp-100) REVERT: E 87 ARG cc_start: 0.9219 (mtt90) cc_final: 0.8756 (ttm-80) REVERT: E 91 ARG cc_start: 0.8881 (mtt180) cc_final: 0.8527 (mtt90) REVERT: E 113 LEU cc_start: 0.9019 (mt) cc_final: 0.8504 (tp) REVERT: F 50 GLN cc_start: 0.9367 (tp40) cc_final: 0.9072 (tm-30) REVERT: F 113 LEU cc_start: 0.8936 (mt) cc_final: 0.8412 (tp) REVERT: G 130 PHE cc_start: 0.6822 (m-80) cc_final: 0.6599 (m-80) REVERT: H 91 ARG cc_start: 0.8839 (mtt180) cc_final: 0.8506 (mtt90) REVERT: H 144 GLN cc_start: 0.9487 (mm110) cc_final: 0.9111 (mm110) outliers start: 53 outliers final: 49 residues processed: 427 average time/residue: 0.7759 time to fit residues: 451.2519 Evaluate side-chains 446 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 396 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 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 547 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 559 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 276 SER Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 171 TYR 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 D residue 540 ASP Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 340 PHE Chi-restraints excluded: chain G residue 381 CYS Chi-restraints excluded: chain G residue 388 ASP 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 136 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 521 GLN G 240 HIS ** G 363 HIS ** 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 = 0.4066 r_free = 0.4066 target = 0.127222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092610 restraints weight = 130142.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.096375 restraints weight = 55654.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098714 restraints weight = 35234.686| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.7456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16044 Z= 0.218 Angle : 0.593 8.458 21680 Z= 0.319 Chirality : 0.034 0.105 2428 Planarity : 0.005 0.110 2732 Dihedral : 3.880 20.219 2148 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.28 % Allowed : 23.91 % Favored : 72.82 % 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: 1.54 (0.19), residues: 1936 helix: 1.36 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : 0.03 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 379 HIS 0.002 0.001 HIS B 240 PHE 0.026 0.001 PHE E 93 TYR 0.016 0.001 TYR A 267 ARG 0.017 0.001 ARG A 533 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8493.48 seconds wall clock time: 149 minutes 32.83 seconds (8972.83 seconds total)