Starting phenix.real_space_refine on Fri Nov 15 09:42:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/11_2024/8jlk_36400.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/11_2024/8jlk_36400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/11_2024/8jlk_36400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/11_2024/8jlk_36400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/11_2024/8jlk_36400.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/11_2024/8jlk_36400.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.084 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 63 5.16 5 C 5617 2.51 5 N 1506 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8824 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1915 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2084 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 255} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1775 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UJL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.90, per 1000 atoms: 0.56 Number of scatterers: 8824 At special positions: 0 Unit cell: (110.4, 134.32, 105.8, 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 63 16.00 O 1638 8.00 N 1506 7.00 C 5617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 15 sheets defined 37.6% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.631A pdb=" N GLU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.683A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.038A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.555A pdb=" N ASN A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 removed outlier: 3.771A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 298 through 318 removed outlier: 4.358A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.859A pdb=" N ARG A 352 " --> pdb=" O ASP A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.841A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 4.195A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 50 removed outlier: 3.573A pdb=" N VAL R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 85 removed outlier: 4.462A pdb=" N MET R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Proline residue: R 77 - end of helix removed outlier: 3.652A pdb=" N THR R 83 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL R 84 " --> pdb=" O MET R 80 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 126 removed outlier: 3.663A pdb=" N CYS R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP R 126 " --> pdb=" O CYS R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 134 removed outlier: 3.695A pdb=" N LYS R 133 " --> pdb=" O ARG R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 159 removed outlier: 3.825A pdb=" N LEU R 149 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 167 through 174 Processing helix chain 'R' and resid 186 through 222 removed outlier: 4.066A pdb=" N VAL R 191 " --> pdb=" O LYS R 187 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE R 200 " --> pdb=" O THR R 196 " (cutoff:3.500A) Proline residue: R 201 - end of helix removed outlier: 4.118A pdb=" N TYR R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE R 214 " --> pdb=" O TYR R 210 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA R 220 " --> pdb=" O ALA R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 260 removed outlier: 4.437A pdb=" N PHE R 257 " --> pdb=" O MET R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 279 through 303 removed outlier: 3.662A pdb=" N ASN R 283 " --> pdb=" O PRO R 279 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) Proline residue: R 298 - end of helix removed outlier: 3.525A pdb=" N TYR R 301 " --> pdb=" O ASN R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 310 removed outlier: 3.755A pdb=" N ARG R 310 " --> pdb=" O PRO R 306 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.841A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 24 removed outlier: 3.690A pdb=" N LYS Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU Y 15 " --> pdb=" O GLN Y 11 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 45 removed outlier: 3.910A pdb=" N LYS Y 32 " --> pdb=" O ILE Y 28 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 190 removed outlier: 4.787A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 9.900A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.891A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.891A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.136A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.053A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.958A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.600A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.515A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.017A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.553A pdb=" N SER S 7 " --> pdb=" O SER S 21 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.573A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.529A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1083 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: 2.65 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1434 1.32 - 1.44: 2537 1.44 - 1.57: 4956 1.57 - 1.69: 0 1.69 - 1.82: 93 Bond restraints: 9020 Sorted by residual: bond pdb=" CA PHE R 264 " pdb=" C PHE R 264 " ideal model delta sigma weight residual 1.524 1.455 0.070 1.24e-02 6.50e+03 3.16e+01 bond pdb=" C GLY R 218 " pdb=" O GLY R 218 " ideal model delta sigma weight residual 1.234 1.287 -0.053 1.20e-02 6.94e+03 1.98e+01 bond pdb=" N ARG R 211 " pdb=" CA ARG R 211 " ideal model delta sigma weight residual 1.459 1.510 -0.051 1.21e-02 6.83e+03 1.74e+01 bond pdb=" C PHE R 264 " pdb=" N PHE R 265 " ideal model delta sigma weight residual 1.335 1.283 0.052 1.34e-02 5.57e+03 1.51e+01 bond pdb=" C ILE R 118 " pdb=" O ILE R 118 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.13e-02 7.83e+03 1.45e+01 ... (remaining 9015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 11827 2.09 - 4.17: 326 4.17 - 6.26: 63 6.26 - 8.35: 10 8.35 - 10.43: 2 Bond angle restraints: 12228 Sorted by residual: angle pdb=" N ARG R 82 " pdb=" CA ARG R 82 " pdb=" C ARG R 82 " ideal model delta sigma weight residual 113.19 123.62 -10.43 1.19e+00 7.06e-01 7.69e+01 angle pdb=" O SER R 117 " pdb=" C SER R 117 " pdb=" N ILE R 118 " ideal model delta sigma weight residual 122.07 115.61 6.46 1.03e+00 9.43e-01 3.94e+01 angle pdb=" C ARG R 211 " pdb=" CA ARG R 211 " pdb=" CB ARG R 211 " ideal model delta sigma weight residual 110.79 101.72 9.07 1.66e+00 3.63e-01 2.99e+01 angle pdb=" CA SER R 117 " pdb=" C SER R 117 " pdb=" N ILE R 118 " ideal model delta sigma weight residual 117.07 123.27 -6.20 1.14e+00 7.69e-01 2.96e+01 angle pdb=" C ILE R 118 " pdb=" N ASP R 119 " pdb=" CA ASP R 119 " ideal model delta sigma weight residual 120.38 113.57 6.81 1.37e+00 5.33e-01 2.47e+01 ... (remaining 12223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4805 17.88 - 35.76: 419 35.76 - 53.63: 94 53.63 - 71.51: 18 71.51 - 89.39: 7 Dihedral angle restraints: 5343 sinusoidal: 2066 harmonic: 3277 Sorted by residual: dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 146.24 -53.24 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CA GLU S 234 " pdb=" C GLU S 234 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " ideal model delta harmonic sigma weight residual -180.00 -157.60 -22.40 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA LEU R 74 " pdb=" C LEU R 74 " pdb=" N ILE R 75 " pdb=" CA ILE R 75 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1054 0.051 - 0.101: 264 0.101 - 0.152: 44 0.152 - 0.203: 6 0.203 - 0.254: 3 Chirality restraints: 1371 Sorted by residual: chirality pdb=" CA ARG R 221 " pdb=" N ARG R 221 " pdb=" C ARG R 221 " pdb=" CB ARG R 221 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA LEU R 282 " pdb=" N LEU R 282 " pdb=" C LEU R 282 " pdb=" CB LEU R 282 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ILE R 278 " pdb=" N ILE R 278 " pdb=" C ILE R 278 " pdb=" CB ILE R 278 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1368 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 UJL R 401 " 0.101 2.00e-02 2.50e+03 8.43e-02 1.24e+02 pdb=" C5 UJL R 401 " -0.063 2.00e-02 2.50e+03 pdb=" C6 UJL R 401 " -0.015 2.00e-02 2.50e+03 pdb=" C7 UJL R 401 " 0.021 2.00e-02 2.50e+03 pdb=" C8 UJL R 401 " 0.111 2.00e-02 2.50e+03 pdb=" C9 UJL R 401 " -0.006 2.00e-02 2.50e+03 pdb=" S1 UJL R 401 " -0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 209 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C TYR R 209 " -0.061 2.00e-02 2.50e+03 pdb=" O TYR R 209 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR R 210 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 286 " 0.018 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LEU R 286 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU R 286 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR R 287 " 0.020 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1168 2.75 - 3.29: 8465 3.29 - 3.83: 13828 3.83 - 4.36: 16148 4.36 - 4.90: 28455 Nonbonded interactions: 68064 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.213 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP Y 48 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR R 55 " pdb=" OD1 ASN R 58 " model vdw 2.253 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.262 3.040 nonbonded pdb=" NH1 ARG B 42 " pdb=" OE1 GLN B 44 " model vdw 2.275 3.120 ... (remaining 68059 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.630 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.980 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 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 : 0.005 0.073 9020 Z= 0.343 Angle : 0.836 10.434 12228 Z= 0.518 Chirality : 0.047 0.254 1371 Planarity : 0.006 0.084 1553 Dihedral : 14.643 89.390 3222 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.95 % Allowed : 0.42 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.25), residues: 1111 helix: 0.38 (0.28), residues: 369 sheet: -0.34 (0.31), residues: 294 loop : -1.63 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP S 47 HIS 0.012 0.002 HIS R 98 PHE 0.027 0.002 PHE S 29 TYR 0.016 0.002 TYR R 305 ARG 0.012 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 258 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.7880 (mt) cc_final: 0.7342 (mt) REVERT: A 230 TYR cc_start: 0.6275 (m-80) cc_final: 0.5914 (m-80) REVERT: R 197 SER cc_start: 0.6763 (t) cc_final: 0.6528 (p) REVERT: S 27 PHE cc_start: 0.6767 (p90) cc_final: 0.6442 (p90) outliers start: 9 outliers final: 4 residues processed: 264 average time/residue: 0.2658 time to fit residues: 92.0728 Evaluate side-chains 158 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 TYR Chi-restraints excluded: chain R residue 211 ARG Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 289 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 324 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** S 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9020 Z= 0.228 Angle : 0.661 8.371 12228 Z= 0.350 Chirality : 0.046 0.160 1371 Planarity : 0.005 0.063 1553 Dihedral : 5.623 59.770 1254 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.21 % Allowed : 12.01 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.25), residues: 1111 helix: 0.64 (0.27), residues: 391 sheet: 0.41 (0.32), residues: 262 loop : -1.86 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP S 47 HIS 0.007 0.001 HIS A 197 PHE 0.013 0.001 PHE B 241 TYR 0.018 0.002 TYR R 287 ARG 0.005 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7559 (ttp) REVERT: A 213 GLN cc_start: 0.7955 (mt0) cc_final: 0.7749 (mt0) REVERT: A 260 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7705 (mtmt) REVERT: R 188 VAL cc_start: 0.8360 (m) cc_final: 0.8093 (p) REVERT: S 34 MET cc_start: 0.7296 (mmm) cc_final: 0.6937 (mmm) REVERT: Y 50 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8073 (mp) outliers start: 21 outliers final: 11 residues processed: 177 average time/residue: 0.2442 time to fit residues: 57.9374 Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain Y residue 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 0.0970 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 ASN ** S 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9020 Z= 0.175 Angle : 0.567 6.279 12228 Z= 0.299 Chirality : 0.043 0.168 1371 Planarity : 0.004 0.049 1553 Dihedral : 4.627 40.766 1248 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.95 % Allowed : 14.65 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1111 helix: 0.99 (0.27), residues: 391 sheet: 0.59 (0.33), residues: 260 loop : -1.73 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 47 HIS 0.003 0.001 HIS A 324 PHE 0.014 0.001 PHE A 343 TYR 0.015 0.001 TYR A 30 ARG 0.009 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7302 (mpp) REVERT: A 213 GLN cc_start: 0.8167 (mt0) cc_final: 0.7938 (mt0) REVERT: A 269 LEU cc_start: 0.5949 (OUTLIER) cc_final: 0.5648 (mt) REVERT: B 212 ASP cc_start: 0.6674 (t0) cc_final: 0.5574 (t0) REVERT: R 188 VAL cc_start: 0.8213 (m) cc_final: 0.7979 (p) REVERT: S 34 MET cc_start: 0.7421 (mmm) cc_final: 0.7046 (mmm) outliers start: 28 outliers final: 13 residues processed: 170 average time/residue: 0.2170 time to fit residues: 50.9872 Evaluate side-chains 152 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 51 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 340 ASN S 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.6801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9020 Z= 0.315 Angle : 0.674 8.271 12228 Z= 0.354 Chirality : 0.046 0.201 1371 Planarity : 0.005 0.049 1553 Dihedral : 5.118 44.817 1244 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.37 % Allowed : 15.60 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.25), residues: 1111 helix: 0.81 (0.26), residues: 388 sheet: 0.45 (0.33), residues: 256 loop : -1.79 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP S 47 HIS 0.005 0.001 HIS A 197 PHE 0.018 0.002 PHE S 29 TYR 0.022 0.002 TYR A 30 ARG 0.006 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7253 (mpp) REVERT: A 269 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5731 (mt) REVERT: A 281 GLU cc_start: 0.7384 (tp30) cc_final: 0.6769 (tp30) REVERT: B 59 TYR cc_start: 0.7970 (m-80) cc_final: 0.7551 (m-80) REVERT: B 188 MET cc_start: 0.8475 (mmt) cc_final: 0.8069 (mmt) REVERT: B 217 MET cc_start: 0.7138 (ttp) cc_final: 0.6900 (ppp) REVERT: R 86 ARG cc_start: 0.7178 (mtt90) cc_final: 0.6861 (mpt180) REVERT: R 188 VAL cc_start: 0.8042 (m) cc_final: 0.7817 (p) REVERT: S 34 MET cc_start: 0.7754 (mmm) cc_final: 0.7493 (mmm) REVERT: S 77 ASN cc_start: 0.6380 (m-40) cc_final: 0.5961 (p0) REVERT: S 82 GLN cc_start: 0.7513 (mm-40) cc_final: 0.7220 (mp10) outliers start: 32 outliers final: 18 residues processed: 183 average time/residue: 0.2115 time to fit residues: 53.1246 Evaluate side-chains 155 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 304 PHE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain Y residue 17 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.0980 chunk 43 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.0030 chunk 26 optimal weight: 8.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.7008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9020 Z= 0.142 Angle : 0.547 6.434 12228 Z= 0.285 Chirality : 0.041 0.160 1371 Planarity : 0.004 0.045 1553 Dihedral : 4.445 41.531 1244 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.21 % Allowed : 18.12 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.25), residues: 1111 helix: 1.42 (0.27), residues: 378 sheet: 0.42 (0.32), residues: 270 loop : -1.62 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP S 47 HIS 0.004 0.001 HIS A 324 PHE 0.017 0.001 PHE B 199 TYR 0.011 0.001 TYR R 287 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7606 (mpp) REVERT: A 269 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.5829 (mt) REVERT: A 281 GLU cc_start: 0.7324 (tp30) cc_final: 0.6695 (tp30) REVERT: B 172 GLU cc_start: 0.6832 (tp30) cc_final: 0.6618 (tm-30) outliers start: 21 outliers final: 10 residues processed: 163 average time/residue: 0.2334 time to fit residues: 51.4155 Evaluate side-chains 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain Y residue 17 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.0170 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 261 GLN B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.7206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9020 Z= 0.157 Angle : 0.553 7.269 12228 Z= 0.289 Chirality : 0.042 0.159 1371 Planarity : 0.004 0.043 1553 Dihedral : 4.215 33.379 1242 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.79 % Allowed : 19.28 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1111 helix: 1.60 (0.27), residues: 378 sheet: 0.45 (0.32), residues: 272 loop : -1.52 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP S 47 HIS 0.006 0.001 HIS A 324 PHE 0.012 0.001 PHE A 343 TYR 0.015 0.001 TYR B 59 ARG 0.010 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7441 (mpp) REVERT: A 184 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7352 (tp) REVERT: A 269 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5675 (mt) REVERT: A 281 GLU cc_start: 0.7355 (tp30) cc_final: 0.6727 (tp30) REVERT: A 357 GLN cc_start: 0.7979 (tt0) cc_final: 0.7689 (tt0) REVERT: S 34 MET cc_start: 0.6709 (mmm) cc_final: 0.6295 (mmm) outliers start: 17 outliers final: 12 residues processed: 161 average time/residue: 0.2252 time to fit residues: 49.0369 Evaluate side-chains 151 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain Y residue 17 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 0.1980 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 0.0270 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.0020 overall best weight: 0.8450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 261 GLN B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.7465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9020 Z= 0.158 Angle : 0.547 7.294 12228 Z= 0.286 Chirality : 0.041 0.159 1371 Planarity : 0.004 0.043 1553 Dihedral : 4.136 33.187 1242 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.42 % Allowed : 19.39 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1111 helix: 1.84 (0.28), residues: 374 sheet: 0.46 (0.32), residues: 273 loop : -1.38 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP S 47 HIS 0.005 0.001 HIS A 324 PHE 0.012 0.001 PHE A 343 TYR 0.014 0.001 TYR A 30 ARG 0.009 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7449 (mpp) REVERT: A 184 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7330 (tp) REVERT: A 269 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5642 (mt) REVERT: A 281 GLU cc_start: 0.7333 (tp30) cc_final: 0.6720 (tp30) REVERT: A 357 GLN cc_start: 0.7961 (tt0) cc_final: 0.7682 (tt0) REVERT: B 227 SER cc_start: 0.8743 (m) cc_final: 0.8516 (t) REVERT: S 34 MET cc_start: 0.6863 (mmm) cc_final: 0.6490 (mmm) outliers start: 23 outliers final: 19 residues processed: 168 average time/residue: 0.2242 time to fit residues: 51.3851 Evaluate side-chains 155 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain Y residue 17 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.7859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9020 Z= 0.293 Angle : 0.642 7.564 12228 Z= 0.338 Chirality : 0.045 0.157 1371 Planarity : 0.005 0.044 1553 Dihedral : 4.759 45.860 1242 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.85 % Allowed : 19.28 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1111 helix: 1.50 (0.27), residues: 377 sheet: 0.39 (0.32), residues: 272 loop : -1.54 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP S 47 HIS 0.010 0.002 HIS A 324 PHE 0.016 0.002 PHE A 343 TYR 0.026 0.002 TYR A 30 ARG 0.007 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7508 (mpp) REVERT: A 184 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7351 (tp) REVERT: A 269 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5680 (mt) REVERT: A 281 GLU cc_start: 0.7253 (tp30) cc_final: 0.6712 (tp30) REVERT: B 59 TYR cc_start: 0.7685 (m-80) cc_final: 0.7319 (m-80) REVERT: S 34 MET cc_start: 0.7290 (mmm) cc_final: 0.7046 (mmm) outliers start: 27 outliers final: 16 residues processed: 164 average time/residue: 0.2262 time to fit residues: 50.3698 Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain Y residue 17 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 59 optimal weight: 0.0870 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.8061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9020 Z= 0.241 Angle : 0.615 8.056 12228 Z= 0.324 Chirality : 0.043 0.157 1371 Planarity : 0.004 0.047 1553 Dihedral : 4.546 39.646 1242 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.21 % Allowed : 20.13 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1111 helix: 1.50 (0.27), residues: 380 sheet: 0.29 (0.32), residues: 273 loop : -1.54 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP S 47 HIS 0.008 0.001 HIS A 324 PHE 0.015 0.002 PHE A 343 TYR 0.023 0.002 TYR A 30 ARG 0.013 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7397 (mpp) REVERT: A 184 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7333 (tp) REVERT: A 269 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5676 (mt) REVERT: A 314 ARG cc_start: 0.7273 (ttm110) cc_final: 0.7051 (ttp80) REVERT: B 59 TYR cc_start: 0.7614 (m-80) cc_final: 0.7359 (m-80) REVERT: B 227 SER cc_start: 0.8948 (m) cc_final: 0.8734 (t) REVERT: R 189 SER cc_start: 0.8397 (m) cc_final: 0.8087 (p) outliers start: 21 outliers final: 17 residues processed: 159 average time/residue: 0.2277 time to fit residues: 49.2433 Evaluate side-chains 152 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain Y residue 17 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.8263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9020 Z= 0.302 Angle : 0.672 7.648 12228 Z= 0.355 Chirality : 0.045 0.189 1371 Planarity : 0.005 0.051 1553 Dihedral : 4.823 48.253 1242 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.74 % Allowed : 20.02 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1111 helix: 1.33 (0.27), residues: 379 sheet: 0.11 (0.31), residues: 272 loop : -1.61 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP S 47 HIS 0.008 0.002 HIS A 324 PHE 0.017 0.002 PHE A 343 TYR 0.026 0.002 TYR A 30 ARG 0.013 0.001 ARG A 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7403 (mpp) REVERT: A 184 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7351 (tp) REVERT: A 269 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5708 (mt) REVERT: B 59 TYR cc_start: 0.7678 (m-80) cc_final: 0.7400 (m-80) REVERT: R 189 SER cc_start: 0.8339 (m) cc_final: 0.8015 (p) outliers start: 26 outliers final: 20 residues processed: 162 average time/residue: 0.2276 time to fit residues: 50.3468 Evaluate side-chains 156 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain Y residue 17 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.0020 chunk 63 optimal weight: 0.9980 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 261 GLN B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.188657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.148930 restraints weight = 11648.911| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.81 r_work: 0.3732 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.8354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9020 Z= 0.178 Angle : 0.603 9.242 12228 Z= 0.314 Chirality : 0.042 0.159 1371 Planarity : 0.004 0.057 1553 Dihedral : 4.353 40.807 1242 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.32 % Allowed : 21.07 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1111 helix: 1.72 (0.27), residues: 374 sheet: 0.16 (0.31), residues: 272 loop : -1.51 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP S 47 HIS 0.005 0.001 HIS A 324 PHE 0.012 0.001 PHE A 343 TYR 0.023 0.001 TYR R 287 ARG 0.014 0.000 ARG A 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2263.86 seconds wall clock time: 50 minutes 56.35 seconds (3056.35 seconds total)