Starting phenix.real_space_refine on Sat Sep 12 14:56:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vhq_32003/09_2026/7vhq_32003.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vhq_32003/09_2026/7vhq_32003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vhq_32003/09_2026/7vhq_32003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vhq_32003/09_2026/7vhq_32003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vhq_32003/09_2026/7vhq_32003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vhq_32003/09_2026/7vhq_32003.map" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 10446 2.51 5 N 2973 2.21 5 O 3186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16650 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "B" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "C" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "D" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "E" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "F" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "G" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "H" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "I" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "U" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "e" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "f" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Time building chain proxies: 3.80, per 1000 atoms: 0.23 Number of scatterers: 16650 At special positions: 0 Unit cell: (176.519, 130.011, 171.234, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 3186 8.00 N 2973 7.00 C 10446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 679.9 milliseconds 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3960 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 29 sheets defined 54.8% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 Processing helix chain 'A' and resid 75 through 84 removed outlier: 4.118A pdb=" N ASP A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 44 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'C' and resid 33 through 43 Processing helix chain 'C' and resid 74 through 84 removed outlier: 3.936A pdb=" N LEU C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 43 Processing helix chain 'D' and resid 75 through 84 removed outlier: 4.102A pdb=" N ASP D 79 " --> pdb=" O PRO D 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 96 Processing helix chain 'E' and resid 169 through 176 removed outlier: 3.554A pdb=" N TYR E 173 " --> pdb=" O ASN E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 199 removed outlier: 3.719A pdb=" N LYS E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR E 199 " --> pdb=" O VAL E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 206 Processing helix chain 'E' and resid 208 through 224 removed outlier: 4.034A pdb=" N ARG E 213 " --> pdb=" O ARG E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 318 removed outlier: 3.816A pdb=" N ALA E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Proline residue: E 277 - end of helix Proline residue: E 313 - end of helix Processing helix chain 'E' and resid 318 through 338 removed outlier: 3.524A pdb=" N THR E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 96 Processing helix chain 'F' and resid 169 through 176 Processing helix chain 'F' and resid 179 through 197 Processing helix chain 'F' and resid 200 through 208 Processing helix chain 'F' and resid 210 through 225 Processing helix chain 'F' and resid 244 through 246 No H-bonds generated for 'chain 'F' and resid 244 through 246' Processing helix chain 'F' and resid 247 through 318 removed outlier: 4.059A pdb=" N ARG F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU F 259 " --> pdb=" O ILE F 255 " (cutoff:3.500A) Proline residue: F 277 - end of helix Proline residue: F 313 - end of helix removed outlier: 3.750A pdb=" N ALA F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 337 removed outlier: 3.709A pdb=" N THR F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 19 removed outlier: 3.505A pdb=" N ILE G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 107 Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 111 through 133 removed outlier: 3.591A pdb=" N ALA G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP G 125 " --> pdb=" O ARG G 121 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG G 133 " --> pdb=" O SER G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 142 Processing helix chain 'G' and resid 145 through 157 Processing helix chain 'G' and resid 216 through 289 removed outlier: 3.577A pdb=" N LEU G 282 " --> pdb=" O GLU G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 308 removed outlier: 3.532A pdb=" N TYR G 294 " --> pdb=" O ASP G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 326 removed outlier: 4.518A pdb=" N TYR G 325 " --> pdb=" O PHE G 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 19 Processing helix chain 'H' and resid 99 through 107 Processing helix chain 'H' and resid 111 through 134 removed outlier: 4.347A pdb=" N ALA H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 141 Processing helix chain 'H' and resid 146 through 156 Processing helix chain 'H' and resid 218 through 288 removed outlier: 3.737A pdb=" N VAL H 234 " --> pdb=" O GLU H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 307 removed outlier: 3.523A pdb=" N TYR H 294 " --> pdb=" O ASP H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 326 removed outlier: 4.472A pdb=" N TYR H 325 " --> pdb=" O PHE H 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 19 Processing helix chain 'I' and resid 99 through 107 Processing helix chain 'I' and resid 111 through 132 removed outlier: 4.438A pdb=" N ALA I 115 " --> pdb=" O ASP I 111 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY I 132 " --> pdb=" O ARG I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 147 removed outlier: 3.599A pdb=" N SER I 143 " --> pdb=" O ILE I 139 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ARG I 144 " --> pdb=" O VAL I 140 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY I 145 " --> pdb=" O THR I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 158 Processing helix chain 'I' and resid 216 through 288 removed outlier: 3.563A pdb=" N VAL I 234 " --> pdb=" O GLU I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 307 Processing helix chain 'I' and resid 321 through 326 removed outlier: 4.553A pdb=" N TYR I 325 " --> pdb=" O PHE I 322 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 96 Processing helix chain 'U' and resid 169 through 176 removed outlier: 3.700A pdb=" N TYR U 173 " --> pdb=" O ASN U 169 " (cutoff:3.500A) Processing helix chain 'U' and resid 179 through 199 removed outlier: 4.013A pdb=" N LYS U 198 " --> pdb=" O GLY U 194 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR U 199 " --> pdb=" O VAL U 195 " (cutoff:3.500A) Processing helix chain 'U' and resid 200 through 228 removed outlier: 7.128A pdb=" N ARG U 209 " --> pdb=" O LEU U 205 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR U 210 " --> pdb=" O THR U 206 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL U 211 " --> pdb=" O GLU U 207 " (cutoff:3.500A) Proline residue: U 226 - end of helix Processing helix chain 'U' and resid 244 through 318 removed outlier: 4.118A pdb=" N ALA U 249 " --> pdb=" O GLU U 245 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ALA U 250 " --> pdb=" O GLU U 246 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN U 262 " --> pdb=" O ARG U 258 " (cutoff:3.500A) Proline residue: U 277 - end of helix Proline residue: U 313 - end of helix removed outlier: 3.558A pdb=" N ALA U 318 " --> pdb=" O GLU U 314 " (cutoff:3.500A) Processing helix chain 'U' and resid 318 through 338 removed outlier: 3.597A pdb=" N THR U 322 " --> pdb=" O ALA U 318 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR U 338 " --> pdb=" O VAL U 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 43 removed outlier: 3.593A pdb=" N PHE e 37 " --> pdb=" O ASP e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 84 removed outlier: 4.453A pdb=" N LEU e 78 " --> pdb=" O ASP e 74 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP e 79 " --> pdb=" O PRO e 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 43 Processing helix chain 'f' and resid 75 through 84 removed outlier: 4.186A pdb=" N ASP f 79 " --> pdb=" O PRO f 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.380A pdb=" N TYR A 69 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG A 47 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL A 89 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 49 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 69 removed outlier: 3.776A pdb=" N GLU B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG B 47 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL B 89 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 49 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 65 through 69 removed outlier: 6.509A pdb=" N ARG C 47 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL C 89 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA C 49 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 65 through 69 removed outlier: 6.445A pdb=" N ARG D 47 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL D 89 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA D 49 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'E' and resid 113 through 118 removed outlier: 4.943A pdb=" N PHE E 114 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG E 110 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU E 131 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 141 through 150 removed outlier: 6.751A pdb=" N GLU E 160 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG E 166 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU E 233 " --> pdb=" O ARG E 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 339 through 341 removed outlier: 5.801A pdb=" N ARG F 339 " --> pdb=" O MET G 314 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS E 340 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL G 315 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU E 342 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG E 339 " --> pdb=" O MET H 314 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET H 316 " --> pdb=" O ARG E 339 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL E 341 " --> pdb=" O MET H 316 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N MET I 314 " --> pdb=" O VAL U 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AB1, first strand: chain 'F' and resid 113 through 118 removed outlier: 5.042A pdb=" N PHE F 114 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG F 110 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS F 116 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 141 through 150 removed outlier: 6.662A pdb=" N ARG F 158 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA F 240 " --> pdb=" O ARG F 158 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU F 160 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N PHE F 238 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN F 162 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL F 236 " --> pdb=" O ASN F 162 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN F 164 " --> pdb=" O LEU F 234 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 20 through 22 Processing sheet with id=AB4, first strand: chain 'G' and resid 27 through 33 Processing sheet with id=AB5, first strand: chain 'G' and resid 39 through 40 Processing sheet with id=AB6, first strand: chain 'G' and resid 70 through 80 removed outlier: 4.059A pdb=" N SER G 91 " --> pdb=" O ASN G 74 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA G 76 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL G 89 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG G 78 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU G 87 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE G 88 " --> pdb=" O ILE G 213 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE G 213 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP G 90 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP G 207 " --> pdb=" O LYS G 94 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG G 96 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL G 205 " --> pdb=" O ARG G 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 21 through 22 Processing sheet with id=AB8, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AB9, first strand: chain 'H' and resid 39 through 40 removed outlier: 3.638A pdb=" N LYS H 44 " --> pdb=" O ASP H 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 70 through 80 removed outlier: 3.959A pdb=" N ALA H 76 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL H 89 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG H 78 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU H 87 " --> pdb=" O ARG H 78 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE H 88 " --> pdb=" O GLN H 212 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN H 212 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP H 90 " --> pdb=" O ILE H 210 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE H 210 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR H 92 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL H 208 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS H 94 " --> pdb=" O VAL H 206 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AC3, first strand: chain 'I' and resid 27 through 28 Processing sheet with id=AC4, first strand: chain 'I' and resid 32 through 33 Processing sheet with id=AC5, first strand: chain 'I' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER I 91 " --> pdb=" O ASN I 74 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER I 91 " --> pdb=" O ASN I 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR I 92 " --> pdb=" O ILE I 210 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE I 210 " --> pdb=" O TYR I 92 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LYS I 94 " --> pdb=" O VAL I 208 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL I 208 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG I 96 " --> pdb=" O VAL I 206 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL I 206 " --> pdb=" O ARG I 96 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 97 through 100 Processing sheet with id=AC8, first strand: chain 'U' and resid 116 through 118 Processing sheet with id=AC9, first strand: chain 'U' and resid 141 through 150 removed outlier: 6.651A pdb=" N GLU U 160 " --> pdb=" O GLN U 239 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG U 166 " --> pdb=" O LEU U 233 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU U 233 " --> pdb=" O ARG U 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'e' and resid 65 through 69 removed outlier: 6.192A pdb=" N ARG e 47 " --> pdb=" O LYS e 87 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL e 89 " --> pdb=" O ARG e 47 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA e 49 " --> pdb=" O VAL e 89 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 65 through 69 removed outlier: 6.488A pdb=" N ARG f 47 " --> pdb=" O LYS f 87 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL f 89 " --> pdb=" O ARG f 47 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA f 49 " --> pdb=" O VAL f 89 " (cutoff:3.500A) 1042 hydrogen bonds defined for protein. 3033 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4497 1.33 - 1.45: 2612 1.45 - 1.57: 9691 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 16890 Sorted by residual: bond pdb=" CA ILE C 70 " pdb=" CB ILE C 70 " ideal model delta sigma weight residual 1.526 1.543 -0.017 1.55e-02 4.16e+03 1.19e+00 bond pdb=" CG GLN A 39 " pdb=" CD GLN A 39 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.09e+00 bond pdb=" CA GLN E 276 " pdb=" C GLN E 276 " ideal model delta sigma weight residual 1.520 1.533 -0.013 1.23e-02 6.61e+03 1.06e+00 bond pdb=" C LYS F 133 " pdb=" O LYS F 133 " ideal model delta sigma weight residual 1.248 1.236 0.013 1.26e-02 6.30e+03 1.02e+00 bond pdb=" CA GLN F 276 " pdb=" C GLN F 276 " ideal model delta sigma weight residual 1.520 1.532 -0.012 1.23e-02 6.61e+03 9.74e-01 ... (remaining 16885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 22127 1.51 - 3.03: 562 3.03 - 4.54: 83 4.54 - 6.06: 20 6.06 - 7.57: 11 Bond angle restraints: 22803 Sorted by residual: angle pdb=" C ASN e 43 " pdb=" N ASP e 44 " pdb=" CA ASP e 44 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 angle pdb=" N GLN A 39 " pdb=" CA GLN A 39 " pdb=" CB GLN A 39 " ideal model delta sigma weight residual 110.39 116.02 -5.63 1.66e+00 3.63e-01 1.15e+01 angle pdb=" N ILE C 70 " pdb=" CA ILE C 70 " pdb=" CB ILE C 70 " ideal model delta sigma weight residual 110.23 113.75 -3.52 1.07e+00 8.73e-01 1.08e+01 angle pdb=" C LEU A 38 " pdb=" N GLN A 39 " pdb=" CA GLN A 39 " ideal model delta sigma weight residual 120.72 115.25 5.47 1.67e+00 3.59e-01 1.07e+01 angle pdb=" CA GLN A 39 " pdb=" CB GLN A 39 " pdb=" CG GLN A 39 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.02e+01 ... (remaining 22798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 9385 17.00 - 34.00: 918 34.00 - 50.99: 151 50.99 - 67.99: 15 67.99 - 84.99: 16 Dihedral angle restraints: 10485 sinusoidal: 4383 harmonic: 6102 Sorted by residual: dihedral pdb=" CA GLY U 208 " pdb=" C GLY U 208 " pdb=" N ARG U 209 " pdb=" CA ARG U 209 " ideal model delta harmonic sigma weight residual -180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLY I 35 " pdb=" C GLY I 35 " pdb=" N LYS I 36 " pdb=" CA LYS I 36 " ideal model delta harmonic sigma weight residual 180.00 -157.75 -22.25 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ASN U 169 " pdb=" C ASN U 169 " pdb=" N PRO U 170 " pdb=" CA PRO U 170 " ideal model delta harmonic sigma weight residual 180.00 -163.77 -16.23 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 10482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1856 0.037 - 0.075: 465 0.075 - 0.112: 212 0.112 - 0.150: 50 0.150 - 0.187: 6 Chirality restraints: 2589 Sorted by residual: chirality pdb=" CA ASP e 44 " pdb=" N ASP e 44 " pdb=" C ASP e 44 " pdb=" CB ASP e 44 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA ILE C 70 " pdb=" N ILE C 70 " pdb=" C ILE C 70 " pdb=" CB ILE C 70 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CA GLN e 39 " pdb=" N GLN e 39 " pdb=" C GLN e 39 " pdb=" CB GLN e 39 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 2586 not shown) Planarity restraints: 2985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 194 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO I 195 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO I 195 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 195 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 74 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO B 75 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN e 43 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C ASN e 43 " -0.027 2.00e-02 2.50e+03 pdb=" O ASN e 43 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP e 44 " 0.009 2.00e-02 2.50e+03 ... (remaining 2982 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 487 2.71 - 3.26: 17159 3.26 - 3.81: 26696 3.81 - 4.35: 31457 4.35 - 4.90: 54908 Nonbonded interactions: 130707 Sorted by model distance: nonbonded pdb=" OE1 GLU e 40 " pdb=" OH TYR e 66 " model vdw 2.165 3.040 nonbonded pdb=" O LYS F 172 " pdb=" OG SER F 176 " model vdw 2.180 3.040 nonbonded pdb=" OG SER I 143 " pdb=" NH2 ARG U 193 " model vdw 2.210 3.120 nonbonded pdb=" OE1 GLN E 164 " pdb=" NZ LYS G 122 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASP G 285 " pdb=" N ALA G 286 " model vdw 2.247 3.120 ... (remaining 130702 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'U' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.210 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.003 0.027 16890 Z= 0.145 Angle : 0.603 7.570 22803 Z= 0.342 Chirality : 0.043 0.187 2589 Planarity : 0.004 0.076 2985 Dihedral : 13.433 84.989 6525 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.19), residues: 2046 helix: 2.44 (0.16), residues: 1037 sheet: 0.93 (0.30), residues: 342 loop : -0.67 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 50 TYR 0.019 0.001 TYR H 17 PHE 0.023 0.001 PHE G 287 TRP 0.023 0.002 TRP U 92 HIS 0.002 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (16890) covalent geometry : angle 0.60329 / 0.34 (22803) hydrogen bonds : bond 0.12369 / 8.67 ( 1037) hydrogen bonds : angle 5.25704 / 3.75 ( 3033) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7890 (ptt180) cc_final: 0.6870 (mmp-170) REVERT: A 87 LYS cc_start: 0.7550 (tmmt) cc_final: 0.7276 (tmmt) REVERT: B 43 ASN cc_start: 0.8520 (t0) cc_final: 0.7792 (t0) REVERT: B 45 GLN cc_start: 0.7881 (mp10) cc_final: 0.6658 (mp10) REVERT: C 36 THR cc_start: 0.8625 (p) cc_final: 0.8410 (p) REVERT: C 40 GLU cc_start: 0.8434 (tt0) cc_final: 0.8128 (tt0) REVERT: C 69 TYR cc_start: 0.4646 (m-80) cc_final: 0.4241 (m-80) REVERT: D 34 TYR cc_start: 0.7956 (t80) cc_final: 0.7721 (t80) REVERT: D 50 ARG cc_start: 0.7677 (ttm110) cc_final: 0.7467 (ttm110) REVERT: D 91 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7130 (mm-30) REVERT: E 331 MET cc_start: 0.8441 (mmt) cc_final: 0.8129 (mmt) REVERT: F 161 MET cc_start: 0.7484 (mmt) cc_final: 0.7077 (mmt) REVERT: G 18 MET cc_start: 0.6861 (mmp) cc_final: 0.6611 (mmm) REVERT: G 43 ASN cc_start: 0.8523 (t0) cc_final: 0.8288 (t0) REVERT: G 221 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7854 (tm-30) REVERT: H 114 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7785 (tm-30) REVERT: I 18 MET cc_start: 0.7549 (tpt) cc_final: 0.7113 (ttm) REVERT: e 79 ASP cc_start: 0.8345 (m-30) cc_final: 0.8129 (m-30) REVERT: f 62 ASP cc_start: 0.8203 (p0) cc_final: 0.7712 (p0) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.1352 time to fit residues: 58.7825 Evaluate side-chains 247 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.0770 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 116 HIS I 70 GLN e 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.092532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072025 restraints weight = 43565.667| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.73 r_work: 0.3157 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16890 Z= 0.129 Angle : 0.540 8.210 22803 Z= 0.292 Chirality : 0.043 0.182 2589 Planarity : 0.004 0.055 2985 Dihedral : 4.116 21.512 2331 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.94 % Allowed : 7.86 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.19), residues: 2046 helix: 2.55 (0.15), residues: 1050 sheet: 0.75 (0.27), residues: 387 loop : -0.65 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 144 TYR 0.021 0.001 TYR e 34 PHE 0.029 0.001 PHE A 37 TRP 0.017 0.001 TRP U 92 HIS 0.002 0.000 HIS U 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (16890) covalent geometry : angle 0.53964 / 0.29 (22803) hydrogen bonds : bond 0.04902 / 3.24 ( 1037) hydrogen bonds : angle 4.28512 / 3.06 ( 3033) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 275 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8023 (mt-10) REVERT: B 45 GLN cc_start: 0.8173 (mp10) cc_final: 0.7510 (mp10) REVERT: C 37 PHE cc_start: 0.7352 (t80) cc_final: 0.7060 (t80) REVERT: C 54 ARG cc_start: 0.7237 (tpt90) cc_final: 0.6998 (tpt90) REVERT: C 69 TYR cc_start: 0.4940 (m-80) cc_final: 0.4611 (m-80) REVERT: C 77 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8659 (tp) REVERT: D 48 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6828 (tm-30) REVERT: D 91 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7484 (mm-30) REVERT: F 161 MET cc_start: 0.7717 (mmt) cc_final: 0.7273 (mmt) REVERT: G 18 MET cc_start: 0.7218 (mmp) cc_final: 0.6781 (mtp) REVERT: G 43 ASN cc_start: 0.8917 (t0) cc_final: 0.8595 (t0) REVERT: G 221 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8114 (tm-30) REVERT: H 114 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7925 (tm-30) REVERT: I 1 MET cc_start: 0.3098 (pmm) cc_final: 0.2687 (ttt) REVERT: I 18 MET cc_start: 0.7434 (tpt) cc_final: 0.6894 (ttm) REVERT: e 39 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8191 (mp10) REVERT: e 69 TYR cc_start: 0.8083 (m-10) cc_final: 0.7865 (m-10) REVERT: e 79 ASP cc_start: 0.8658 (m-30) cc_final: 0.8414 (m-30) REVERT: e 87 LYS cc_start: 0.8356 (tptp) cc_final: 0.8121 (tptp) REVERT: f 62 ASP cc_start: 0.8454 (p0) cc_final: 0.7949 (p0) outliers start: 17 outliers final: 12 residues processed: 278 average time/residue: 0.1356 time to fit residues: 57.1058 Evaluate side-chains 257 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 54 PHE Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 39 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 38 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 104 optimal weight: 0.4980 chunk 157 optimal weight: 1.9990 chunk 172 optimal weight: 0.0970 chunk 14 optimal weight: 4.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 GLN I 70 GLN e 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.092471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.071860 restraints weight = 43826.342| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.75 r_work: 0.3152 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16890 Z= 0.125 Angle : 0.518 7.540 22803 Z= 0.281 Chirality : 0.043 0.168 2589 Planarity : 0.003 0.044 2985 Dihedral : 4.041 22.256 2331 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.50 % Allowed : 10.19 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.19), residues: 2046 helix: 2.64 (0.15), residues: 1050 sheet: 0.84 (0.27), residues: 380 loop : -0.66 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 30 TYR 0.028 0.001 TYR D 34 PHE 0.032 0.001 PHE A 37 TRP 0.015 0.001 TRP U 92 HIS 0.008 0.001 HIS F 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (16890) covalent geometry : angle 0.51845 / 0.28 (22803) hydrogen bonds : bond 0.04748 / 3.13 ( 1037) hydrogen bonds : angle 4.17309 / 2.98 ( 3033) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 257 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 84 LYS cc_start: 0.7069 (mtpp) cc_final: 0.6791 (ptpt) REVERT: B 40 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8081 (mt-10) REVERT: B 43 ASN cc_start: 0.8873 (t0) cc_final: 0.8523 (t0) REVERT: B 45 GLN cc_start: 0.8286 (mp10) cc_final: 0.7194 (mp10) REVERT: B 48 GLU cc_start: 0.7627 (pm20) cc_final: 0.7029 (pm20) REVERT: C 38 LEU cc_start: 0.8804 (tt) cc_final: 0.8444 (pp) REVERT: C 82 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7264 (pp) REVERT: D 34 TYR cc_start: 0.8145 (t80) cc_final: 0.7731 (t80) REVERT: D 50 ARG cc_start: 0.7491 (ttp-110) cc_final: 0.7285 (ttm110) REVERT: D 91 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7726 (mm-30) REVERT: F 149 MET cc_start: 0.8332 (mmm) cc_final: 0.7032 (mpp) REVERT: F 161 MET cc_start: 0.7795 (mmt) cc_final: 0.7289 (mmt) REVERT: G 18 MET cc_start: 0.7243 (mmp) cc_final: 0.6732 (mtp) REVERT: G 43 ASN cc_start: 0.8905 (t0) cc_final: 0.8626 (t0) REVERT: G 221 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8084 (tm-30) REVERT: H 72 MET cc_start: 0.8814 (ptm) cc_final: 0.8448 (ptm) REVERT: H 114 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7933 (tm-30) REVERT: H 314 MET cc_start: 0.8493 (ttm) cc_final: 0.8187 (mtp) REVERT: e 39 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: e 79 ASP cc_start: 0.8660 (m-30) cc_final: 0.8427 (m-30) REVERT: f 62 ASP cc_start: 0.8489 (p0) cc_final: 0.7926 (p0) outliers start: 27 outliers final: 12 residues processed: 266 average time/residue: 0.1270 time to fit residues: 51.4475 Evaluate side-chains 258 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 244 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 54 PHE Chi-restraints excluded: chain U residue 179 SER Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 39 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 80 ASN C 52 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 GLN e 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.090531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.069777 restraints weight = 43547.072| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.73 r_work: 0.3103 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16890 Z= 0.178 Angle : 0.553 11.169 22803 Z= 0.300 Chirality : 0.044 0.194 2589 Planarity : 0.004 0.040 2985 Dihedral : 4.139 21.153 2331 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.05 % Allowed : 12.35 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.19), residues: 2046 helix: 2.53 (0.15), residues: 1051 sheet: 0.79 (0.27), residues: 380 loop : -0.69 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 54 TYR 0.018 0.001 TYR D 34 PHE 0.033 0.002 PHE A 37 TRP 0.014 0.001 TRP U 92 HIS 0.002 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (16890) covalent geometry : angle 0.55293 / 0.30 (22803) hydrogen bonds : bond 0.05124 / 3.37 ( 1037) hydrogen bonds : angle 4.25041 / 3.02 ( 3033) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7535 (t80) REVERT: A 38 LEU cc_start: 0.8807 (mm) cc_final: 0.8504 (mm) REVERT: B 40 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8071 (mt-10) REVERT: B 43 ASN cc_start: 0.8903 (t0) cc_final: 0.8468 (t0) REVERT: B 45 GLN cc_start: 0.8319 (mp10) cc_final: 0.7153 (mp10) REVERT: B 48 GLU cc_start: 0.7658 (pm20) cc_final: 0.6981 (pm20) REVERT: C 30 ARG cc_start: 0.5702 (ttt-90) cc_final: 0.5437 (ttt-90) REVERT: C 38 LEU cc_start: 0.8805 (tt) cc_final: 0.8461 (pp) REVERT: C 82 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7445 (pp) REVERT: D 34 TYR cc_start: 0.8218 (t80) cc_final: 0.7849 (t80) REVERT: D 48 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6703 (tm-30) REVERT: D 50 ARG cc_start: 0.7529 (ttp-110) cc_final: 0.7306 (ttp-110) REVERT: D 91 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8071 (mm-30) REVERT: F 161 MET cc_start: 0.7824 (mmt) cc_final: 0.7309 (mmt) REVERT: G 18 MET cc_start: 0.7225 (mmp) cc_final: 0.6754 (mtp) REVERT: G 43 ASN cc_start: 0.8916 (t0) cc_final: 0.8623 (t0) REVERT: G 70 GLN cc_start: 0.8717 (mp-120) cc_final: 0.8052 (mp10) REVERT: G 221 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8184 (tm-30) REVERT: H 87 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8765 (pp) REVERT: H 114 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7968 (tm-30) REVERT: H 314 MET cc_start: 0.8583 (ttm) cc_final: 0.8282 (mtp) REVERT: I 1 MET cc_start: 0.3500 (pmm) cc_final: 0.3280 (ttt) REVERT: I 18 MET cc_start: 0.7396 (tpt) cc_final: 0.6862 (ttt) REVERT: U 263 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8533 (tm-30) REVERT: e 79 ASP cc_start: 0.8740 (m-30) cc_final: 0.8515 (m-30) REVERT: e 87 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8257 (tptp) REVERT: f 62 ASP cc_start: 0.8534 (p0) cc_final: 0.7989 (p0) outliers start: 37 outliers final: 22 residues processed: 269 average time/residue: 0.1316 time to fit residues: 54.4049 Evaluate side-chains 266 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 54 PHE Chi-restraints excluded: chain U residue 135 VAL Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain U residue 179 SER Chi-restraints excluded: chain e residue 87 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 168 optimal weight: 0.0040 chunk 9 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 172 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 139 optimal weight: 0.0170 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.5032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 80 ASN ** E 337 ASN ** 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 = 0.3670 r_free = 0.3670 target = 0.092012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.071387 restraints weight = 43474.600| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.74 r_work: 0.3141 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16890 Z= 0.120 Angle : 0.515 8.706 22803 Z= 0.279 Chirality : 0.043 0.159 2589 Planarity : 0.003 0.039 2985 Dihedral : 4.021 22.024 2331 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.77 % Allowed : 13.46 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.19), residues: 2046 helix: 2.62 (0.15), residues: 1050 sheet: 0.86 (0.28), residues: 369 loop : -0.63 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 54 TYR 0.015 0.001 TYR C 66 PHE 0.031 0.001 PHE U 111 TRP 0.016 0.001 TRP U 92 HIS 0.001 0.000 HIS E 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (16890) covalent geometry : angle 0.51459 / 0.28 (22803) hydrogen bonds : bond 0.04734 / 3.10 ( 1037) hydrogen bonds : angle 4.11090 / 2.93 ( 3033) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8223 (t80) cc_final: 0.7601 (t80) REVERT: A 37 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7530 (t80) REVERT: A 45 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7521 (tm-30) REVERT: A 58 VAL cc_start: 0.6902 (OUTLIER) cc_final: 0.6651 (t) REVERT: B 39 GLN cc_start: 0.8329 (tp40) cc_final: 0.8072 (tp40) REVERT: B 40 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7914 (mt-10) REVERT: B 45 GLN cc_start: 0.8332 (mp10) cc_final: 0.7518 (mp10) REVERT: C 30 ARG cc_start: 0.5988 (ttt-90) cc_final: 0.5742 (ttt-90) REVERT: C 38 LEU cc_start: 0.8756 (tt) cc_final: 0.8318 (pp) REVERT: C 54 ARG cc_start: 0.7647 (tpt90) cc_final: 0.7440 (tpt90) REVERT: C 82 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7397 (pp) REVERT: D 34 TYR cc_start: 0.8143 (t80) cc_final: 0.7671 (t80) REVERT: D 74 ASP cc_start: 0.8680 (t0) cc_final: 0.8472 (t0) REVERT: F 228 ASP cc_start: 0.8723 (t0) cc_final: 0.8273 (t0) REVERT: G 18 MET cc_start: 0.7098 (mmp) cc_final: 0.6682 (mtp) REVERT: G 43 ASN cc_start: 0.8882 (t0) cc_final: 0.8582 (t0) REVERT: G 70 GLN cc_start: 0.8581 (mp-120) cc_final: 0.8016 (mp10) REVERT: G 221 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8088 (tm-30) REVERT: G 227 MET cc_start: 0.8890 (mtm) cc_final: 0.8642 (mtp) REVERT: H 87 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8730 (pp) REVERT: H 114 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7958 (tm-30) REVERT: H 314 MET cc_start: 0.8634 (ttm) cc_final: 0.8324 (mtp) REVERT: U 263 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8542 (tm-30) REVERT: e 79 ASP cc_start: 0.8718 (m-30) cc_final: 0.8477 (m-30) REVERT: e 87 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8303 (tptp) REVERT: f 62 ASP cc_start: 0.8513 (p0) cc_final: 0.7902 (p0) outliers start: 32 outliers final: 16 residues processed: 271 average time/residue: 0.1193 time to fit residues: 49.7738 Evaluate side-chains 262 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 54 PHE Chi-restraints excluded: chain U residue 135 VAL Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 87 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 15 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 0.0000 chunk 49 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN B 80 ASN C 80 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.092201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.071655 restraints weight = 43569.834| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.75 r_work: 0.3148 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16890 Z= 0.122 Angle : 0.527 12.894 22803 Z= 0.283 Chirality : 0.043 0.174 2589 Planarity : 0.003 0.041 2985 Dihedral : 3.948 22.082 2331 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.77 % Allowed : 14.40 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.19), residues: 2046 helix: 2.66 (0.15), residues: 1051 sheet: 0.88 (0.27), residues: 369 loop : -0.61 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 54 TYR 0.026 0.001 TYR e 34 PHE 0.032 0.001 PHE U 111 TRP 0.018 0.001 TRP E 92 HIS 0.001 0.000 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (16890) covalent geometry : angle 0.52728 / 0.28 (22803) hydrogen bonds : bond 0.04651 / 3.04 ( 1037) hydrogen bonds : angle 4.05830 / 2.90 ( 3033) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8151 (t80) cc_final: 0.7325 (t80) REVERT: A 47 ARG cc_start: 0.7359 (ptt90) cc_final: 0.6674 (mmp-170) REVERT: B 39 GLN cc_start: 0.8351 (tp40) cc_final: 0.8116 (tp40) REVERT: B 40 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7908 (mt-10) REVERT: B 45 GLN cc_start: 0.8412 (mp10) cc_final: 0.7591 (mp10) REVERT: B 48 GLU cc_start: 0.7590 (pm20) cc_final: 0.6984 (pm20) REVERT: C 30 ARG cc_start: 0.5953 (ttt-90) cc_final: 0.5698 (ttt-90) REVERT: C 38 LEU cc_start: 0.8743 (tt) cc_final: 0.8329 (pp) REVERT: D 34 TYR cc_start: 0.8192 (t80) cc_final: 0.7837 (t80) REVERT: F 228 ASP cc_start: 0.8651 (t0) cc_final: 0.8214 (t0) REVERT: G 18 MET cc_start: 0.7015 (mmp) cc_final: 0.6608 (mtp) REVERT: G 43 ASN cc_start: 0.8871 (t0) cc_final: 0.8561 (t0) REVERT: G 70 GLN cc_start: 0.8565 (mp-120) cc_final: 0.8038 (mp10) REVERT: G 227 MET cc_start: 0.8910 (mtm) cc_final: 0.8665 (mtp) REVERT: H 87 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8751 (pp) REVERT: H 114 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7945 (tm-30) REVERT: H 314 MET cc_start: 0.8637 (ttm) cc_final: 0.8329 (mtp) REVERT: U 263 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8565 (tm-30) REVERT: U 296 GLN cc_start: 0.8916 (tt0) cc_final: 0.8701 (tt0) REVERT: e 42 ASN cc_start: 0.9131 (m110) cc_final: 0.8886 (m-40) REVERT: e 79 ASP cc_start: 0.8726 (m-30) cc_final: 0.8482 (m-30) REVERT: e 87 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8386 (tptp) REVERT: f 62 ASP cc_start: 0.8506 (p0) cc_final: 0.7887 (p0) outliers start: 32 outliers final: 22 residues processed: 265 average time/residue: 0.1247 time to fit residues: 51.0158 Evaluate side-chains 263 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 54 PHE Chi-restraints excluded: chain U residue 135 VAL Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain U residue 179 SER Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 87 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 118 optimal weight: 0.0370 chunk 196 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 187 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.092214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.071580 restraints weight = 43728.470| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.75 r_work: 0.3145 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16890 Z= 0.126 Angle : 0.534 10.571 22803 Z= 0.286 Chirality : 0.043 0.189 2589 Planarity : 0.003 0.041 2985 Dihedral : 3.941 21.296 2331 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.88 % Allowed : 14.62 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.19), residues: 2046 helix: 2.65 (0.15), residues: 1051 sheet: 0.82 (0.27), residues: 370 loop : -0.62 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 54 TYR 0.015 0.001 TYR C 66 PHE 0.033 0.001 PHE U 111 TRP 0.015 0.001 TRP U 92 HIS 0.001 0.000 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (16890) covalent geometry : angle 0.53391 / 0.29 (22803) hydrogen bonds : bond 0.04653 / 3.04 ( 1037) hydrogen bonds : angle 4.06270 / 2.90 ( 3033) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8079 (t80) cc_final: 0.7354 (t80) REVERT: A 37 PHE cc_start: 0.7785 (t80) cc_final: 0.7554 (t80) REVERT: B 39 GLN cc_start: 0.8384 (tp40) cc_final: 0.8138 (tp40) REVERT: B 45 GLN cc_start: 0.8460 (mp10) cc_final: 0.7630 (mp10) REVERT: B 55 GLU cc_start: 0.7440 (mp0) cc_final: 0.7186 (mp0) REVERT: B 69 TYR cc_start: 0.8614 (m-10) cc_final: 0.8153 (m-80) REVERT: C 30 ARG cc_start: 0.5931 (ttt-90) cc_final: 0.5671 (ttt-90) REVERT: C 38 LEU cc_start: 0.8708 (tt) cc_final: 0.8309 (pp) REVERT: C 45 GLN cc_start: 0.6376 (tm-30) cc_final: 0.6102 (tm-30) REVERT: F 149 MET cc_start: 0.8654 (mmm) cc_final: 0.8160 (mtp) REVERT: F 228 ASP cc_start: 0.8692 (t0) cc_final: 0.8241 (t70) REVERT: G 18 MET cc_start: 0.7017 (mmp) cc_final: 0.6601 (mtp) REVERT: G 43 ASN cc_start: 0.8864 (t0) cc_final: 0.8553 (t0) REVERT: G 70 GLN cc_start: 0.8565 (mp-120) cc_final: 0.8016 (mp10) REVERT: H 87 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8782 (pp) REVERT: H 114 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7952 (tm-30) REVERT: H 314 MET cc_start: 0.8619 (ttm) cc_final: 0.8304 (mtp) REVERT: U 263 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8561 (tm-30) REVERT: U 296 GLN cc_start: 0.8917 (tt0) cc_final: 0.8696 (tt0) REVERT: e 79 ASP cc_start: 0.8722 (m-30) cc_final: 0.8483 (m-30) REVERT: e 87 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8471 (tptp) REVERT: f 62 ASP cc_start: 0.8503 (p0) cc_final: 0.7884 (p0) outliers start: 34 outliers final: 22 residues processed: 268 average time/residue: 0.1173 time to fit residues: 48.2159 Evaluate side-chains 265 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 54 PHE Chi-restraints excluded: chain U residue 135 VAL Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 179 SER Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 87 LYS Chi-restraints excluded: chain f residue 48 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 55 optimal weight: 5.9990 chunk 34 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.697 > 50:) chunk 18 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.091779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.071033 restraints weight = 43925.385| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.76 r_work: 0.3135 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16890 Z= 0.137 Angle : 0.554 12.852 22803 Z= 0.295 Chirality : 0.043 0.202 2589 Planarity : 0.003 0.061 2985 Dihedral : 3.989 21.717 2331 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.77 % Allowed : 14.78 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.19), residues: 2046 helix: 2.62 (0.15), residues: 1053 sheet: 0.81 (0.27), residues: 370 loop : -0.64 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 65 TYR 0.016 0.001 TYR H 17 PHE 0.035 0.001 PHE U 111 TRP 0.020 0.001 TRP U 92 HIS 0.002 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (16890) covalent geometry : angle 0.55439 / 0.30 (22803) hydrogen bonds : bond 0.04767 / 3.11 ( 1037) hydrogen bonds : angle 4.09514 / 2.93 ( 3033) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7681 (ptt90) cc_final: 0.6729 (mmp-170) REVERT: B 39 GLN cc_start: 0.8332 (tp40) cc_final: 0.8129 (tm-30) REVERT: B 40 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7953 (mt-10) REVERT: B 45 GLN cc_start: 0.8443 (mp10) cc_final: 0.7569 (mp10) REVERT: B 48 GLU cc_start: 0.7553 (pm20) cc_final: 0.7043 (pm20) REVERT: B 69 TYR cc_start: 0.8599 (m-10) cc_final: 0.8120 (m-80) REVERT: C 38 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8302 (pp) REVERT: C 45 GLN cc_start: 0.6374 (tm-30) cc_final: 0.6071 (tm-30) REVERT: D 84 LYS cc_start: 0.8904 (mttt) cc_final: 0.8658 (mtpt) REVERT: F 149 MET cc_start: 0.8685 (mmm) cc_final: 0.8076 (mtp) REVERT: F 228 ASP cc_start: 0.8698 (t0) cc_final: 0.8245 (t70) REVERT: G 18 MET cc_start: 0.7024 (mmp) cc_final: 0.6596 (mtp) REVERT: G 43 ASN cc_start: 0.8853 (t0) cc_final: 0.8538 (t0) REVERT: G 70 GLN cc_start: 0.8615 (mp-120) cc_final: 0.8037 (mp10) REVERT: H 87 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8841 (pp) REVERT: H 114 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7987 (tm-30) REVERT: H 314 MET cc_start: 0.8594 (ttm) cc_final: 0.8339 (mtp) REVERT: I 18 MET cc_start: 0.7344 (tpt) cc_final: 0.6899 (ttt) REVERT: U 161 MET cc_start: 0.8935 (mmt) cc_final: 0.8726 (mmt) REVERT: U 263 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8541 (tm-30) REVERT: e 79 ASP cc_start: 0.8724 (m-30) cc_final: 0.8482 (m-30) REVERT: e 87 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8450 (tptp) REVERT: f 62 ASP cc_start: 0.8512 (p0) cc_final: 0.7896 (p0) outliers start: 32 outliers final: 23 residues processed: 258 average time/residue: 0.1313 time to fit residues: 52.0303 Evaluate side-chains 262 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 54 PHE Chi-restraints excluded: chain U residue 135 VAL Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 179 SER Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 87 LYS Chi-restraints excluded: chain f residue 48 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 9 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.091448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.070725 restraints weight = 43666.193| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.75 r_work: 0.3128 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16890 Z= 0.145 Angle : 0.565 11.905 22803 Z= 0.300 Chirality : 0.044 0.324 2589 Planarity : 0.003 0.066 2985 Dihedral : 4.027 21.596 2331 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.44 % Allowed : 15.23 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.19), residues: 2046 helix: 2.60 (0.15), residues: 1053 sheet: 0.78 (0.27), residues: 369 loop : -0.68 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 30 TYR 0.015 0.001 TYR C 66 PHE 0.036 0.001 PHE U 111 TRP 0.022 0.001 TRP U 92 HIS 0.002 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (16890) covalent geometry : angle 0.56544 / 0.30 (22803) hydrogen bonds : bond 0.04842 / 3.16 ( 1037) hydrogen bonds : angle 4.13477 / 2.95 ( 3033) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 39 GLN cc_start: 0.8330 (tp40) cc_final: 0.8107 (tm-30) REVERT: B 40 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7940 (mt-10) REVERT: B 45 GLN cc_start: 0.8438 (mp10) cc_final: 0.7568 (mp10) REVERT: B 48 GLU cc_start: 0.7577 (pm20) cc_final: 0.6999 (pm20) REVERT: B 55 GLU cc_start: 0.7533 (mp0) cc_final: 0.7284 (mp0) REVERT: B 69 TYR cc_start: 0.8585 (m-10) cc_final: 0.8089 (m-80) REVERT: C 38 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8332 (pp) REVERT: C 45 GLN cc_start: 0.6361 (tm-30) cc_final: 0.6074 (tm-30) REVERT: D 84 LYS cc_start: 0.8906 (mttt) cc_final: 0.8611 (mtpt) REVERT: F 149 MET cc_start: 0.8702 (mmm) cc_final: 0.8070 (mtp) REVERT: F 228 ASP cc_start: 0.8699 (t0) cc_final: 0.8220 (t70) REVERT: G 18 MET cc_start: 0.6974 (mmp) cc_final: 0.6530 (mtp) REVERT: G 43 ASN cc_start: 0.8838 (t0) cc_final: 0.8531 (t0) REVERT: G 70 GLN cc_start: 0.8622 (mp-120) cc_final: 0.8038 (mp10) REVERT: H 87 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8884 (pp) REVERT: H 314 MET cc_start: 0.8608 (ttm) cc_final: 0.8342 (mtp) REVERT: I 18 MET cc_start: 0.7341 (tpt) cc_final: 0.6889 (ttt) REVERT: U 161 MET cc_start: 0.8947 (mmt) cc_final: 0.8725 (mmt) REVERT: U 263 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8527 (tm-30) REVERT: e 42 ASN cc_start: 0.9151 (m110) cc_final: 0.8900 (m-40) REVERT: e 79 ASP cc_start: 0.8719 (m-30) cc_final: 0.8478 (m-30) REVERT: e 87 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8465 (tptp) REVERT: f 62 ASP cc_start: 0.8514 (p0) cc_final: 0.7900 (p0) outliers start: 26 outliers final: 21 residues processed: 260 average time/residue: 0.1286 time to fit residues: 51.8230 Evaluate side-chains 261 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 54 PHE Chi-restraints excluded: chain U residue 135 VAL Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 179 SER Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 87 LYS Chi-restraints excluded: chain f residue 48 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 112 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.091235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.070591 restraints weight = 43622.128| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.75 r_work: 0.3122 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16890 Z= 0.150 Angle : 0.583 12.801 22803 Z= 0.310 Chirality : 0.045 0.331 2589 Planarity : 0.003 0.056 2985 Dihedral : 4.047 21.166 2331 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.44 % Allowed : 15.56 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.19), residues: 2046 helix: 2.61 (0.15), residues: 1052 sheet: 0.72 (0.27), residues: 370 loop : -0.69 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 54 TYR 0.029 0.001 TYR e 34 PHE 0.037 0.001 PHE U 111 TRP 0.026 0.002 TRP U 92 HIS 0.002 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (16890) covalent geometry : angle 0.58331 / 0.31 (22803) hydrogen bonds : bond 0.04903 / 3.20 ( 1037) hydrogen bonds : angle 4.13910 / 2.95 ( 3033) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 GLN cc_start: 0.8400 (tp40) cc_final: 0.8148 (tm-30) REVERT: B 40 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8171 (mt-10) REVERT: B 45 GLN cc_start: 0.8420 (mp10) cc_final: 0.7981 (mp10) REVERT: B 48 GLU cc_start: 0.7539 (pm20) cc_final: 0.6998 (pm20) REVERT: B 55 GLU cc_start: 0.7485 (mp0) cc_final: 0.7226 (mp0) REVERT: B 69 TYR cc_start: 0.8587 (m-10) cc_final: 0.8004 (m-80) REVERT: C 38 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8340 (pp) REVERT: C 45 GLN cc_start: 0.6248 (tm-30) cc_final: 0.6031 (tm-30) REVERT: D 74 ASP cc_start: 0.8122 (t0) cc_final: 0.7766 (t0) REVERT: D 84 LYS cc_start: 0.8905 (mttt) cc_final: 0.8604 (mtpt) REVERT: F 149 MET cc_start: 0.8728 (mmm) cc_final: 0.8060 (mtp) REVERT: F 228 ASP cc_start: 0.8684 (t0) cc_final: 0.8197 (t70) REVERT: G 18 MET cc_start: 0.7030 (mmp) cc_final: 0.6573 (mtp) REVERT: G 43 ASN cc_start: 0.8842 (t0) cc_final: 0.8534 (t0) REVERT: G 70 GLN cc_start: 0.8654 (mp-120) cc_final: 0.8056 (mp10) REVERT: H 87 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8910 (pp) REVERT: H 314 MET cc_start: 0.8604 (ttm) cc_final: 0.8337 (mtp) REVERT: I 18 MET cc_start: 0.7277 (tpt) cc_final: 0.6893 (ttt) REVERT: I 32 LEU cc_start: 0.8106 (tp) cc_final: 0.7875 (pp) REVERT: I 58 PHE cc_start: 0.7914 (m-80) cc_final: 0.7422 (m-10) REVERT: U 161 MET cc_start: 0.8948 (mmt) cc_final: 0.8734 (mmt) REVERT: U 263 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8533 (tm-30) REVERT: e 42 ASN cc_start: 0.9135 (m110) cc_final: 0.8890 (m-40) REVERT: e 45 GLN cc_start: 0.8912 (mt0) cc_final: 0.8293 (mt0) REVERT: e 79 ASP cc_start: 0.8726 (m-30) cc_final: 0.8482 (m-30) REVERT: e 87 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8301 (tptp) REVERT: f 62 ASP cc_start: 0.8518 (p0) cc_final: 0.7928 (p0) outliers start: 26 outliers final: 23 residues processed: 257 average time/residue: 0.1304 time to fit residues: 51.3912 Evaluate side-chains 261 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 54 PHE Chi-restraints excluded: chain U residue 135 VAL Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 149 MET Chi-restraints excluded: chain U residue 179 SER Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 87 LYS Chi-restraints excluded: chain f residue 48 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 171 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.091219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070587 restraints weight = 43740.116| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.75 r_work: 0.3122 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16890 Z= 0.150 Angle : 0.593 13.771 22803 Z= 0.314 Chirality : 0.045 0.364 2589 Planarity : 0.004 0.064 2985 Dihedral : 4.063 21.358 2331 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.61 % Allowed : 15.61 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.19), residues: 2046 helix: 2.57 (0.15), residues: 1058 sheet: 0.72 (0.27), residues: 369 loop : -0.77 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 30 TYR 0.017 0.001 TYR H 17 PHE 0.037 0.001 PHE U 111 TRP 0.029 0.002 TRP U 92 HIS 0.002 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (16890) covalent geometry : angle 0.59309 / 0.31 (22803) hydrogen bonds : bond 0.04920 / 3.20 ( 1037) hydrogen bonds : angle 4.15174 / 2.96 ( 3033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4295.08 seconds wall clock time: 74 minutes 16.51 seconds (4456.51 seconds total)