Starting phenix.real_space_refine on Sat Dec 28 19:17:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwm_37893/12_2024/8wwm_37893.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwm_37893/12_2024/8wwm_37893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wwm_37893/12_2024/8wwm_37893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwm_37893/12_2024/8wwm_37893.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwm_37893/12_2024/8wwm_37893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwm_37893/12_2024/8wwm_37893.cif" } resolution = 2.81 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= 0.001 sd= 0.063 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 68 5.16 5 C 5708 2.51 5 N 1517 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8963 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2238 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 139 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 5.06, per 1000 atoms: 0.56 Number of scatterers: 8963 At special positions: 0 Unit cell: (88.81, 115.56, 128.4, 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 68 16.00 O 1670 8.00 N 1517 7.00 C 5708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 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: 2.44 Conformation dependent library (CDL) restraints added in 1.3 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 38.0% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.606A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.062A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.862A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.632A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.974A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.524A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 108 through 136 removed outlier: 3.893A pdb=" N MET R 112 " --> pdb=" O ILE R 108 " (cutoff:3.500A) Proline residue: R 113 - end of helix Processing helix chain 'R' and resid 145 through 164 removed outlier: 3.909A pdb=" N PHE R 150 " --> pdb=" O VAL R 146 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE R 152 " --> pdb=" O ASP R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 174 removed outlier: 6.177A pdb=" N GLN R 171 " --> pdb=" O PHE R 167 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU R 172 " --> pdb=" O MET R 168 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY R 174 " --> pdb=" O HIS R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 216 removed outlier: 3.753A pdb=" N MET R 184 " --> pdb=" O PHE R 180 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR R 186 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU R 187 " --> pdb=" O THR R 183 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER R 199 " --> pdb=" O SER R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 223 removed outlier: 3.538A pdb=" N THR R 221 " --> pdb=" O ILE R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 244 removed outlier: 3.514A pdb=" N ALA R 238 " --> pdb=" O CYS R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 250 removed outlier: 3.502A pdb=" N TRP R 248 " --> pdb=" O ILE R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 286 removed outlier: 3.849A pdb=" N LEU R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR R 275 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TRP R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 277 " --> pdb=" O ASP R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 303 Processing helix chain 'R' and resid 313 through 348 Proline residue: R 340 - end of helix removed outlier: 3.753A pdb=" N GLN R 345 " --> pdb=" O TYR R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 355 through 384 removed outlier: 4.226A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) Proline residue: R 377 - end of helix Processing helix chain 'R' and resid 384 through 395 removed outlier: 3.646A pdb=" N ARG R 388 " --> pdb=" O CYS R 384 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS R 389 " --> pdb=" O GLU R 385 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER R 394 " --> pdb=" O ARG R 390 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL R 395 " --> pdb=" O LEU R 391 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.254A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.427A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.540A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.975A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.305A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.891A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.481A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.646A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.743A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.141A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.573A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 251 through 255 Processing sheet with id=AB6, first strand: chain 'L' and resid 8 through 9 removed outlier: 3.648A pdb=" N VAL L 12 " --> pdb=" O LEU L 9 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1263 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: 2.67 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2887 1.34 - 1.46: 2082 1.46 - 1.58: 4086 1.58 - 1.70: 0 1.70 - 1.81: 99 Bond restraints: 9154 Sorted by residual: bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.56e+00 bond pdb=" CG1 ILE B 81 " pdb=" CD1 ILE B 81 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.00e+00 bond pdb=" CG LEU B 318 " pdb=" CD1 LEU B 318 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.45e-01 bond pdb=" CB TRP B 211 " pdb=" CG TRP B 211 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.45e-01 bond pdb=" CG LEU B 318 " pdb=" CD2 LEU B 318 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 6.97e-01 ... (remaining 9149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 12130 1.27 - 2.55: 238 2.55 - 3.82: 42 3.82 - 5.09: 11 5.09 - 6.37: 3 Bond angle restraints: 12424 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.64 -4.10 1.91e+00 2.74e-01 4.62e+00 angle pdb=" CA LEU B 318 " pdb=" CB LEU B 318 " pdb=" CG LEU B 318 " ideal model delta sigma weight residual 116.30 122.57 -6.27 3.50e+00 8.16e-02 3.21e+00 angle pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" C TYR E 102 " ideal model delta sigma weight residual 108.74 106.39 2.35 1.38e+00 5.25e-01 2.91e+00 angle pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " pdb=" CG LEU B 190 " ideal model delta sigma weight residual 116.30 121.92 -5.62 3.50e+00 8.16e-02 2.58e+00 angle pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta sigma weight residual 122.11 124.43 -2.32 1.59e+00 3.96e-01 2.14e+00 ... (remaining 12419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 5203 17.10 - 34.20: 179 34.20 - 51.30: 32 51.30 - 68.40: 8 68.40 - 85.49: 2 Dihedral angle restraints: 5424 sinusoidal: 2058 harmonic: 3366 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA HIS E 35 " pdb=" C HIS E 35 " pdb=" N TRP E 36 " pdb=" CA TRP E 36 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 760 0.028 - 0.055: 427 0.055 - 0.083: 137 0.083 - 0.110: 76 0.110 - 0.138: 26 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA THR B 87 " pdb=" N THR B 87 " pdb=" C THR B 87 " pdb=" CB THR B 87 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 1423 not shown) Planarity restraints: 1571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO B 236 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO C 49 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 71 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.57e+00 pdb=" C VAL B 71 " 0.022 2.00e-02 2.50e+03 pdb=" O VAL B 71 " -0.008 2.00e-02 2.50e+03 pdb=" N SER B 72 " -0.007 2.00e-02 2.50e+03 ... (remaining 1568 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1277 2.75 - 3.29: 8560 3.29 - 3.83: 15134 3.83 - 4.36: 18994 4.36 - 4.90: 32634 Nonbonded interactions: 76599 Sorted by model distance: nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.218 3.040 nonbonded pdb=" NE2 GLN R 196 " pdb=" OH TYR R 342 " model vdw 2.220 3.120 nonbonded pdb=" O ILE R 149 " pdb=" ND2 ASN R 153 " model vdw 2.222 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.230 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.236 3.040 ... (remaining 76594 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: 0.810 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.680 Find NCS groups from input model: 0.090 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:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 : 0.004 0.049 9154 Z= 0.281 Angle : 0.482 6.368 12424 Z= 0.253 Chirality : 0.042 0.138 1426 Planarity : 0.004 0.049 1571 Dihedral : 9.438 85.494 3240 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.93 % Allowed : 3.10 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.24), residues: 1144 helix: 0.73 (0.26), residues: 393 sheet: 0.62 (0.29), residues: 296 loop : 0.01 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 339 HIS 0.004 0.001 HIS B 91 PHE 0.013 0.002 PHE B 199 TYR 0.011 0.002 TYR R 280 ARG 0.004 0.001 ARG L 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 209 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8293 (mttt) cc_final: 0.7899 (mmtm) REVERT: A 21 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7618 (mtm110) REVERT: A 22 ASN cc_start: 0.8108 (m-40) cc_final: 0.7847 (m110) REVERT: A 29 LYS cc_start: 0.8529 (tttt) cc_final: 0.7733 (mtmt) REVERT: A 208 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7693 (ttp80) REVERT: A 275 GLU cc_start: 0.8055 (tt0) cc_final: 0.7772 (tm-30) REVERT: A 306 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7539 (mm-40) REVERT: A 349 LYS cc_start: 0.7671 (mttt) cc_final: 0.7301 (mtmt) REVERT: B 42 ARG cc_start: 0.7286 (tpt170) cc_final: 0.7014 (tmt170) REVERT: B 48 ARG cc_start: 0.8239 (mmt180) cc_final: 0.7859 (mmt180) REVERT: B 52 ARG cc_start: 0.8385 (mtt-85) cc_final: 0.8151 (mtt90) REVERT: B 129 ARG cc_start: 0.7944 (mtp180) cc_final: 0.7465 (ttt90) REVERT: B 153 ASP cc_start: 0.8910 (p0) cc_final: 0.8664 (p0) REVERT: B 226 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7471 (mm-30) REVERT: B 293 ASN cc_start: 0.8344 (m-40) cc_final: 0.8044 (m-40) REVERT: C 21 MET cc_start: 0.7538 (mmm) cc_final: 0.7325 (mtm) REVERT: C 47 GLU cc_start: 0.7532 (pt0) cc_final: 0.7153 (pm20) REVERT: E 21 SER cc_start: 0.8747 (m) cc_final: 0.8503 (t) REVERT: E 63 THR cc_start: 0.8049 (t) cc_final: 0.7769 (p) REVERT: E 186 GLN cc_start: 0.8346 (tt0) cc_final: 0.8029 (tt0) REVERT: R 163 LEU cc_start: 0.6719 (mt) cc_final: 0.6497 (mt) REVERT: R 322 ARG cc_start: 0.6325 (mtt180) cc_final: 0.6076 (mtm-85) REVERT: R 345 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6960 (mp10) outliers start: 9 outliers final: 4 residues processed: 215 average time/residue: 1.2090 time to fit residues: 278.1668 Evaluate side-chains 151 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.0060 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 176 GLN E 179 GLN E 183 GLN E 194 ASN R 194 ASN R 281 GLN R 345 GLN R 348 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9154 Z= 0.194 Angle : 0.569 11.727 12424 Z= 0.298 Chirality : 0.043 0.161 1426 Planarity : 0.004 0.047 1571 Dihedral : 5.436 72.229 1262 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.72 % Allowed : 11.78 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1144 helix: 1.78 (0.26), residues: 387 sheet: 0.71 (0.30), residues: 284 loop : -0.11 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.014 0.001 PHE R 241 TYR 0.023 0.002 TYR R 275 ARG 0.007 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8283 (mttt) cc_final: 0.7864 (mmtm) REVERT: A 18 MET cc_start: 0.8432 (mtp) cc_final: 0.8197 (mtp) REVERT: A 21 ARG cc_start: 0.7633 (ttm170) cc_final: 0.7330 (mtm110) REVERT: A 28 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6315 (mm-30) REVERT: A 29 LYS cc_start: 0.8482 (tttt) cc_final: 0.7805 (ttmt) REVERT: A 186 GLU cc_start: 0.8072 (tt0) cc_final: 0.7615 (mt-10) REVERT: A 208 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7496 (ttp80) REVERT: A 330 LYS cc_start: 0.6761 (mttt) cc_final: 0.5840 (tttm) REVERT: A 349 LYS cc_start: 0.7531 (mttt) cc_final: 0.7175 (mtmt) REVERT: B 42 ARG cc_start: 0.7332 (tpt170) cc_final: 0.7020 (tmt170) REVERT: B 46 ARG cc_start: 0.7564 (mtp-110) cc_final: 0.7359 (mtm-85) REVERT: B 52 ARG cc_start: 0.8458 (mtt-85) cc_final: 0.8095 (mtt90) REVERT: B 61 MET cc_start: 0.8777 (ppp) cc_final: 0.8576 (ppp) REVERT: B 129 ARG cc_start: 0.7905 (mtp180) cc_final: 0.7508 (ttt90) REVERT: B 153 ASP cc_start: 0.8951 (p0) cc_final: 0.8684 (p0) REVERT: B 217 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8309 (pmt) REVERT: B 226 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7442 (mm-30) REVERT: C 47 GLU cc_start: 0.7470 (pt0) cc_final: 0.7104 (pm20) REVERT: E 21 SER cc_start: 0.8426 (m) cc_final: 0.8212 (t) REVERT: E 186 GLN cc_start: 0.8353 (tt0) cc_final: 0.8060 (tm-30) REVERT: R 112 MET cc_start: 0.3861 (mpp) cc_final: 0.3303 (mmt) REVERT: R 163 LEU cc_start: 0.6679 (mt) cc_final: 0.6364 (mt) REVERT: R 345 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6888 (mp10) REVERT: L 8 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7123 (tpp) REVERT: L 14 ARG cc_start: 0.6039 (ptm-80) cc_final: 0.5758 (ppt170) outliers start: 36 outliers final: 8 residues processed: 170 average time/residue: 1.3008 time to fit residues: 235.2331 Evaluate side-chains 149 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain L residue 8 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS R 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9154 Z= 0.229 Angle : 0.539 8.451 12424 Z= 0.287 Chirality : 0.043 0.165 1426 Planarity : 0.004 0.048 1571 Dihedral : 5.346 62.569 1262 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.31 % Allowed : 13.12 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.95 (0.25), residues: 1144 helix: 1.94 (0.27), residues: 384 sheet: 0.29 (0.29), residues: 285 loop : -0.17 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS B 91 PHE 0.012 0.001 PHE R 150 TYR 0.012 0.001 TYR R 275 ARG 0.011 0.001 ARG R 299 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8274 (mttt) cc_final: 0.7908 (mmtm) REVERT: A 18 MET cc_start: 0.8454 (mtp) cc_final: 0.8218 (mtp) REVERT: A 21 ARG cc_start: 0.7635 (ttm170) cc_final: 0.7360 (mtm110) REVERT: A 28 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6829 (mt-10) REVERT: A 29 LYS cc_start: 0.8510 (tttt) cc_final: 0.7582 (mtmt) REVERT: A 46 LYS cc_start: 0.6482 (OUTLIER) cc_final: 0.5956 (ttmt) REVERT: A 186 GLU cc_start: 0.8038 (tt0) cc_final: 0.7663 (mt-10) REVERT: A 208 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7624 (ttp80) REVERT: A 271 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7107 (pttp) REVERT: A 308 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7796 (mt-10) REVERT: A 330 LYS cc_start: 0.6758 (mttt) cc_final: 0.5829 (tttm) REVERT: A 349 LYS cc_start: 0.7544 (mttt) cc_final: 0.7216 (mttt) REVERT: B 42 ARG cc_start: 0.7321 (tpt170) cc_final: 0.7020 (tmt170) REVERT: B 52 ARG cc_start: 0.8514 (mtt-85) cc_final: 0.8181 (mtt90) REVERT: B 129 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7560 (ttt90) REVERT: B 153 ASP cc_start: 0.8931 (p0) cc_final: 0.8669 (p0) REVERT: B 217 MET cc_start: 0.8688 (pmm) cc_final: 0.8449 (pmt) REVERT: B 226 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7454 (mp0) REVERT: B 241 PHE cc_start: 0.9197 (p90) cc_final: 0.8892 (p90) REVERT: C 47 GLU cc_start: 0.7499 (pt0) cc_final: 0.7029 (pm20) REVERT: E 21 SER cc_start: 0.8423 (m) cc_final: 0.8191 (t) REVERT: E 186 GLN cc_start: 0.8316 (tt0) cc_final: 0.8077 (tm-30) REVERT: R 163 LEU cc_start: 0.6606 (mt) cc_final: 0.6295 (mt) REVERT: R 165 MET cc_start: 0.5538 (ttt) cc_final: 0.5284 (tpt) REVERT: R 208 ILE cc_start: 0.6656 (mt) cc_final: 0.5982 (pt) REVERT: L 8 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7158 (tpp) REVERT: L 14 ARG cc_start: 0.6135 (ptm-80) cc_final: 0.5696 (ppt170) outliers start: 32 outliers final: 13 residues processed: 166 average time/residue: 1.3497 time to fit residues: 238.0743 Evaluate side-chains 158 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 393 LEU Chi-restraints excluded: chain L residue 8 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9154 Z= 0.184 Angle : 0.526 8.550 12424 Z= 0.275 Chirality : 0.042 0.204 1426 Planarity : 0.004 0.049 1571 Dihedral : 4.676 50.338 1259 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.79 % Allowed : 15.60 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1144 helix: 2.03 (0.27), residues: 383 sheet: 0.23 (0.29), residues: 282 loop : -0.22 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.011 0.001 PHE R 150 TYR 0.011 0.001 TYR E 190 ARG 0.006 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8294 (mttt) cc_final: 0.7926 (mmtm) REVERT: A 21 ARG cc_start: 0.7566 (ttm170) cc_final: 0.7314 (mtm110) REVERT: A 22 ASN cc_start: 0.7931 (m-40) cc_final: 0.7637 (m110) REVERT: A 29 LYS cc_start: 0.8432 (tttt) cc_final: 0.7501 (mtmt) REVERT: A 186 GLU cc_start: 0.8005 (tt0) cc_final: 0.7649 (mt-10) REVERT: A 207 GLU cc_start: 0.7398 (tt0) cc_final: 0.7165 (tt0) REVERT: A 208 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7402 (ttp80) REVERT: A 209 LYS cc_start: 0.8193 (pttm) cc_final: 0.7634 (ptmt) REVERT: A 271 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.7066 (pttp) REVERT: A 330 LYS cc_start: 0.6744 (mttt) cc_final: 0.5781 (tttm) REVERT: A 349 LYS cc_start: 0.7539 (mttt) cc_final: 0.7169 (mtmt) REVERT: B 42 ARG cc_start: 0.7319 (tpt170) cc_final: 0.7013 (tmt170) REVERT: B 52 ARG cc_start: 0.8515 (mtt-85) cc_final: 0.8188 (mtt90) REVERT: B 129 ARG cc_start: 0.7944 (mtp180) cc_final: 0.7517 (ttt90) REVERT: B 153 ASP cc_start: 0.8947 (p0) cc_final: 0.8667 (p0) REVERT: B 217 MET cc_start: 0.8597 (pmm) cc_final: 0.8356 (pmm) REVERT: B 226 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7408 (mp0) REVERT: B 241 PHE cc_start: 0.9166 (p90) cc_final: 0.8865 (p90) REVERT: C 47 GLU cc_start: 0.7433 (pt0) cc_final: 0.6921 (pm20) REVERT: E 186 GLN cc_start: 0.8397 (tt0) cc_final: 0.8109 (tm-30) REVERT: R 163 LEU cc_start: 0.6611 (mt) cc_final: 0.6286 (mt) REVERT: R 208 ILE cc_start: 0.6818 (mt) cc_final: 0.6131 (pt) REVERT: L 8 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.7072 (mmt) REVERT: L 14 ARG cc_start: 0.6008 (ptm-80) cc_final: 0.5639 (ppt170) outliers start: 27 outliers final: 14 residues processed: 158 average time/residue: 1.3645 time to fit residues: 228.8412 Evaluate side-chains 157 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 8 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 0.0770 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 220 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9154 Z= 0.237 Angle : 0.537 8.206 12424 Z= 0.283 Chirality : 0.043 0.146 1426 Planarity : 0.004 0.049 1571 Dihedral : 4.778 50.164 1259 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.13 % Allowed : 14.67 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.92 (0.25), residues: 1144 helix: 2.16 (0.27), residues: 374 sheet: 0.08 (0.29), residues: 290 loop : -0.22 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS B 91 PHE 0.019 0.001 PHE R 161 TYR 0.010 0.001 TYR E 103 ARG 0.007 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8284 (mttt) cc_final: 0.7928 (mmtm) REVERT: A 21 ARG cc_start: 0.7618 (ttm170) cc_final: 0.7319 (mtm110) REVERT: A 22 ASN cc_start: 0.8014 (m-40) cc_final: 0.7687 (m110) REVERT: A 29 LYS cc_start: 0.8448 (tttt) cc_final: 0.7612 (ttmt) REVERT: A 186 GLU cc_start: 0.8024 (tt0) cc_final: 0.7663 (mt-10) REVERT: A 208 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7454 (ttp80) REVERT: A 271 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.7103 (pttp) REVERT: A 330 LYS cc_start: 0.6764 (mttt) cc_final: 0.5807 (tttm) REVERT: A 349 LYS cc_start: 0.7559 (mttt) cc_final: 0.7166 (mtmt) REVERT: B 42 ARG cc_start: 0.7174 (tpt170) cc_final: 0.6869 (tmt170) REVERT: B 52 ARG cc_start: 0.8536 (mtt-85) cc_final: 0.8213 (mtt90) REVERT: B 129 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7544 (ttt90) REVERT: B 153 ASP cc_start: 0.9000 (p0) cc_final: 0.8698 (p0) REVERT: B 217 MET cc_start: 0.8590 (pmm) cc_final: 0.8384 (pmm) REVERT: B 226 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7484 (mm-30) REVERT: B 241 PHE cc_start: 0.9168 (p90) cc_final: 0.8865 (p90) REVERT: C 47 GLU cc_start: 0.7526 (pt0) cc_final: 0.6973 (pm20) REVERT: E 6 GLU cc_start: 0.7936 (mp0) cc_final: 0.7667 (mp0) REVERT: E 46 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: E 186 GLN cc_start: 0.8413 (tt0) cc_final: 0.8121 (tm-30) REVERT: R 208 ILE cc_start: 0.6817 (mt) cc_final: 0.6129 (pt) REVERT: R 210 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7031 (mtp85) REVERT: R 280 TYR cc_start: 0.6473 (OUTLIER) cc_final: 0.6182 (p90) REVERT: L 8 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7108 (mmt) outliers start: 40 outliers final: 13 residues processed: 159 average time/residue: 1.4235 time to fit residues: 240.5185 Evaluate side-chains 151 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 210 ARG Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain L residue 8 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9154 Z= 0.197 Angle : 0.527 8.153 12424 Z= 0.274 Chirality : 0.043 0.198 1426 Planarity : 0.004 0.049 1571 Dihedral : 4.659 48.480 1259 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.20 % Allowed : 17.05 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.95 (0.25), residues: 1144 helix: 2.23 (0.27), residues: 373 sheet: 0.09 (0.29), residues: 289 loop : -0.24 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.014 0.001 PHE R 161 TYR 0.011 0.001 TYR A 296 ARG 0.005 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8286 (mttt) cc_final: 0.7932 (mmtm) REVERT: A 21 ARG cc_start: 0.7617 (ttm170) cc_final: 0.7350 (mtm110) REVERT: A 22 ASN cc_start: 0.7998 (m-40) cc_final: 0.7686 (m110) REVERT: A 28 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6410 (mm-30) REVERT: A 29 LYS cc_start: 0.8452 (tttt) cc_final: 0.7751 (ttmm) REVERT: A 186 GLU cc_start: 0.8008 (tt0) cc_final: 0.7660 (mt-10) REVERT: A 208 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7440 (ttp80) REVERT: A 271 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.7105 (pttp) REVERT: A 275 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8006 (tp30) REVERT: A 330 LYS cc_start: 0.6739 (mttt) cc_final: 0.5789 (tttm) REVERT: A 349 LYS cc_start: 0.7554 (mttt) cc_final: 0.7158 (mtmt) REVERT: B 42 ARG cc_start: 0.7173 (tpt170) cc_final: 0.6863 (tmt170) REVERT: B 52 ARG cc_start: 0.8533 (mtt-85) cc_final: 0.8241 (mtt90) REVERT: B 129 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7548 (ttt90) REVERT: B 226 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7472 (mp0) REVERT: B 241 PHE cc_start: 0.9173 (p90) cc_final: 0.8880 (p90) REVERT: C 47 GLU cc_start: 0.7470 (pt0) cc_final: 0.6888 (pm20) REVERT: E 46 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: E 186 GLN cc_start: 0.8415 (tt0) cc_final: 0.8132 (tm-30) REVERT: R 192 ASP cc_start: 0.5652 (OUTLIER) cc_final: 0.4665 (t70) REVERT: R 208 ILE cc_start: 0.6875 (mt) cc_final: 0.6188 (pt) REVERT: R 210 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7049 (mtp85) REVERT: R 280 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.6258 (p90) REVERT: L 14 ARG cc_start: 0.6297 (ttp80) cc_final: 0.5910 (ppt170) outliers start: 31 outliers final: 13 residues processed: 152 average time/residue: 1.4446 time to fit residues: 232.7105 Evaluate side-chains 153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 192 ASP Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 210 ARG Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 0.0970 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 108 optimal weight: 0.0570 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9154 Z= 0.157 Angle : 0.515 8.944 12424 Z= 0.265 Chirality : 0.042 0.174 1426 Planarity : 0.004 0.049 1571 Dihedral : 4.475 45.981 1259 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.48 % Allowed : 18.18 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1144 helix: 2.21 (0.27), residues: 376 sheet: 0.22 (0.29), residues: 283 loop : -0.24 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.014 0.001 PHE R 161 TYR 0.011 0.001 TYR E 190 ARG 0.005 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8343 (mttt) cc_final: 0.7940 (mmtm) REVERT: A 21 ARG cc_start: 0.7601 (ttm170) cc_final: 0.7337 (mtm110) REVERT: A 22 ASN cc_start: 0.7999 (m-40) cc_final: 0.7685 (m110) REVERT: A 28 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6302 (mm-30) REVERT: A 29 LYS cc_start: 0.8448 (tttt) cc_final: 0.7744 (ttmm) REVERT: A 53 MET cc_start: 0.7326 (mtt) cc_final: 0.6685 (mtm) REVERT: A 186 GLU cc_start: 0.7985 (tt0) cc_final: 0.7638 (mt-10) REVERT: A 208 ARG cc_start: 0.7719 (ttm-80) cc_final: 0.7369 (ttp80) REVERT: A 283 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6856 (tt) REVERT: A 330 LYS cc_start: 0.6711 (mttt) cc_final: 0.5720 (tttm) REVERT: A 349 LYS cc_start: 0.7554 (mttt) cc_final: 0.7175 (mtmt) REVERT: B 42 ARG cc_start: 0.7141 (tpt170) cc_final: 0.6880 (tmt170) REVERT: B 52 ARG cc_start: 0.8528 (mtt-85) cc_final: 0.8242 (mtt90) REVERT: B 129 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7557 (ttt90) REVERT: B 153 ASP cc_start: 0.8913 (p0) cc_final: 0.8585 (p0) REVERT: B 207 SER cc_start: 0.7900 (p) cc_final: 0.7603 (m) REVERT: B 217 MET cc_start: 0.8696 (pmm) cc_final: 0.8475 (pmt) REVERT: B 226 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7465 (mp0) REVERT: B 241 PHE cc_start: 0.9129 (p90) cc_final: 0.8820 (p90) REVERT: C 47 GLU cc_start: 0.7413 (pt0) cc_final: 0.6783 (pm20) REVERT: E 186 GLN cc_start: 0.8408 (tt0) cc_final: 0.8142 (tm-30) REVERT: R 122 LEU cc_start: 0.7132 (mt) cc_final: 0.6915 (mp) REVERT: R 208 ILE cc_start: 0.6753 (mt) cc_final: 0.6062 (pt) REVERT: R 210 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7109 (mtp85) REVERT: R 280 TYR cc_start: 0.6433 (OUTLIER) cc_final: 0.6166 (p90) REVERT: L 14 ARG cc_start: 0.6240 (ttp80) cc_final: 0.5840 (ppt170) outliers start: 24 outliers final: 11 residues processed: 158 average time/residue: 1.3266 time to fit residues: 222.9997 Evaluate side-chains 153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 210 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 99 optimal weight: 0.0000 chunk 104 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9154 Z= 0.216 Angle : 0.541 8.930 12424 Z= 0.277 Chirality : 0.043 0.160 1426 Planarity : 0.004 0.059 1571 Dihedral : 4.598 45.980 1259 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.00 % Allowed : 18.60 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.95 (0.25), residues: 1144 helix: 2.19 (0.27), residues: 377 sheet: 0.14 (0.29), residues: 285 loop : -0.26 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.012 0.001 PHE R 161 TYR 0.010 0.001 TYR E 190 ARG 0.016 0.001 ARG R 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8354 (mttt) cc_final: 0.7989 (mmtm) REVERT: A 21 ARG cc_start: 0.7629 (ttm170) cc_final: 0.7391 (mtm110) REVERT: A 22 ASN cc_start: 0.8016 (m-40) cc_final: 0.7708 (m110) REVERT: A 28 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6336 (mm-30) REVERT: A 29 LYS cc_start: 0.8459 (tttt) cc_final: 0.7542 (mtmt) REVERT: A 53 MET cc_start: 0.7325 (mtt) cc_final: 0.6763 (mtm) REVERT: A 186 GLU cc_start: 0.8021 (tt0) cc_final: 0.7673 (mt-10) REVERT: A 208 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7392 (ttp80) REVERT: A 251 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7451 (t0) REVERT: A 275 GLU cc_start: 0.8280 (tm-30) cc_final: 0.8055 (tp30) REVERT: A 283 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6940 (tt) REVERT: A 330 LYS cc_start: 0.6726 (mttt) cc_final: 0.5749 (tttm) REVERT: A 349 LYS cc_start: 0.7532 (mttt) cc_final: 0.7150 (mtmt) REVERT: B 42 ARG cc_start: 0.7154 (tpt170) cc_final: 0.6862 (tmt170) REVERT: B 129 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7537 (ttt90) REVERT: B 217 MET cc_start: 0.8681 (pmm) cc_final: 0.8444 (pmt) REVERT: B 226 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7453 (mp0) REVERT: B 241 PHE cc_start: 0.9159 (p90) cc_final: 0.8879 (p90) REVERT: C 47 GLU cc_start: 0.7464 (pt0) cc_final: 0.6849 (pm20) REVERT: E 46 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: E 186 GLN cc_start: 0.8432 (tt0) cc_final: 0.8146 (tm-30) REVERT: R 122 LEU cc_start: 0.7154 (mt) cc_final: 0.6938 (mp) REVERT: R 173 MET cc_start: 0.6134 (mmm) cc_final: 0.5879 (ptm) REVERT: R 192 ASP cc_start: 0.5652 (OUTLIER) cc_final: 0.4678 (t70) REVERT: R 208 ILE cc_start: 0.6814 (mt) cc_final: 0.6099 (pt) REVERT: R 210 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7020 (mtp85) REVERT: R 280 TYR cc_start: 0.6467 (OUTLIER) cc_final: 0.6205 (p90) REVERT: L 14 ARG cc_start: 0.6305 (ttp80) cc_final: 0.5961 (ppt170) outliers start: 29 outliers final: 14 residues processed: 152 average time/residue: 1.3853 time to fit residues: 223.5186 Evaluate side-chains 156 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 192 ASP Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 210 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 79 optimal weight: 0.0270 chunk 31 optimal weight: 0.2980 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9154 Z= 0.154 Angle : 0.528 12.474 12424 Z= 0.267 Chirality : 0.042 0.152 1426 Planarity : 0.004 0.047 1571 Dihedral : 4.406 43.438 1259 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.58 % Allowed : 18.90 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1144 helix: 2.23 (0.27), residues: 377 sheet: 0.22 (0.29), residues: 290 loop : -0.19 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS B 91 PHE 0.012 0.001 PHE R 161 TYR 0.011 0.001 TYR E 190 ARG 0.008 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8343 (mttt) cc_final: 0.7942 (mmtm) REVERT: A 21 ARG cc_start: 0.7596 (ttm170) cc_final: 0.7342 (mtm110) REVERT: A 22 ASN cc_start: 0.7997 (m-40) cc_final: 0.7688 (m110) REVERT: A 28 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6311 (mm-30) REVERT: A 29 LYS cc_start: 0.8440 (tttt) cc_final: 0.7738 (ttmm) REVERT: A 53 MET cc_start: 0.7281 (mtt) cc_final: 0.6753 (mtm) REVERT: A 186 GLU cc_start: 0.7991 (tt0) cc_final: 0.7649 (mt-10) REVERT: A 208 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7367 (ttp80) REVERT: A 251 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7471 (t0) REVERT: A 283 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6844 (tt) REVERT: A 330 LYS cc_start: 0.6750 (mttt) cc_final: 0.5741 (tttm) REVERT: A 349 LYS cc_start: 0.7536 (mttt) cc_final: 0.7228 (mtmt) REVERT: B 42 ARG cc_start: 0.7100 (tpt170) cc_final: 0.6859 (tmt170) REVERT: B 129 ARG cc_start: 0.7945 (mtp180) cc_final: 0.7553 (ttt90) REVERT: B 153 ASP cc_start: 0.8941 (p0) cc_final: 0.8615 (p0) REVERT: B 207 SER cc_start: 0.7899 (p) cc_final: 0.7604 (m) REVERT: B 217 MET cc_start: 0.8665 (pmm) cc_final: 0.8425 (pmt) REVERT: B 226 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7453 (mp0) REVERT: B 241 PHE cc_start: 0.9105 (p90) cc_final: 0.8810 (p90) REVERT: C 47 GLU cc_start: 0.7415 (pt0) cc_final: 0.6768 (pm20) REVERT: E 34 MET cc_start: 0.8570 (mmp) cc_final: 0.8361 (mmm) REVERT: E 186 GLN cc_start: 0.8417 (tt0) cc_final: 0.8144 (tm-30) REVERT: R 122 LEU cc_start: 0.7030 (mt) cc_final: 0.6809 (mp) REVERT: R 191 MET cc_start: 0.6505 (tpp) cc_final: 0.5290 (tmm) REVERT: R 192 ASP cc_start: 0.5654 (OUTLIER) cc_final: 0.4706 (t70) REVERT: R 208 ILE cc_start: 0.6847 (mt) cc_final: 0.6149 (pt) REVERT: R 209 ASP cc_start: 0.6794 (OUTLIER) cc_final: 0.6485 (t0) REVERT: R 210 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7071 (mtp85) REVERT: R 280 TYR cc_start: 0.6424 (OUTLIER) cc_final: 0.6180 (p90) REVERT: R 322 ARG cc_start: 0.6334 (mtm-85) cc_final: 0.5858 (mtm180) REVERT: L 14 ARG cc_start: 0.6245 (ttp80) cc_final: 0.5991 (ppt170) outliers start: 25 outliers final: 13 residues processed: 152 average time/residue: 1.3516 time to fit residues: 218.2763 Evaluate side-chains 156 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 192 ASP Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 210 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.0010 chunk 112 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9154 Z= 0.173 Angle : 0.541 11.475 12424 Z= 0.272 Chirality : 0.042 0.150 1426 Planarity : 0.004 0.075 1571 Dihedral : 4.426 42.894 1259 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.27 % Allowed : 19.32 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1144 helix: 2.27 (0.27), residues: 375 sheet: 0.24 (0.29), residues: 295 loop : -0.19 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS B 91 PHE 0.012 0.001 PHE R 161 TYR 0.011 0.001 TYR E 190 ARG 0.019 0.001 ARG R 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8311 (mttt) cc_final: 0.7922 (mmtm) REVERT: A 21 ARG cc_start: 0.7617 (ttm170) cc_final: 0.7362 (mtm110) REVERT: A 22 ASN cc_start: 0.8002 (m-40) cc_final: 0.7692 (m110) REVERT: A 28 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6317 (mm-30) REVERT: A 29 LYS cc_start: 0.8442 (tttt) cc_final: 0.7529 (mtmt) REVERT: A 53 MET cc_start: 0.7239 (mtt) cc_final: 0.6814 (mtm) REVERT: A 186 GLU cc_start: 0.7994 (tt0) cc_final: 0.7655 (mt-10) REVERT: A 208 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7394 (ttp80) REVERT: A 275 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8086 (tp30) REVERT: A 283 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6850 (tt) REVERT: A 330 LYS cc_start: 0.6796 (mttt) cc_final: 0.5749 (tttm) REVERT: A 349 LYS cc_start: 0.7543 (mttt) cc_final: 0.7230 (mtmt) REVERT: B 42 ARG cc_start: 0.7087 (tpt170) cc_final: 0.6826 (tmt170) REVERT: B 129 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7552 (ttt90) REVERT: B 207 SER cc_start: 0.7895 (p) cc_final: 0.7604 (m) REVERT: B 217 MET cc_start: 0.8587 (pmm) cc_final: 0.8353 (pmt) REVERT: B 226 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7467 (mp0) REVERT: B 241 PHE cc_start: 0.9160 (p90) cc_final: 0.8875 (p90) REVERT: B 293 ASN cc_start: 0.8137 (m-40) cc_final: 0.7833 (m-40) REVERT: C 47 GLU cc_start: 0.7416 (pt0) cc_final: 0.7076 (pm20) REVERT: E 186 GLN cc_start: 0.8422 (tt0) cc_final: 0.8145 (tm-30) REVERT: R 122 LEU cc_start: 0.7004 (mt) cc_final: 0.6793 (mp) REVERT: R 191 MET cc_start: 0.6397 (tpp) cc_final: 0.5203 (tmm) REVERT: R 192 ASP cc_start: 0.5658 (OUTLIER) cc_final: 0.4714 (t70) REVERT: R 208 ILE cc_start: 0.6900 (mt) cc_final: 0.6203 (pt) REVERT: R 209 ASP cc_start: 0.6815 (OUTLIER) cc_final: 0.6533 (t0) REVERT: R 210 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7047 (mtp85) REVERT: R 280 TYR cc_start: 0.6446 (OUTLIER) cc_final: 0.6203 (p90) REVERT: L 14 ARG cc_start: 0.6260 (ttp80) cc_final: 0.5968 (ppt170) outliers start: 22 outliers final: 15 residues processed: 150 average time/residue: 1.3944 time to fit residues: 222.3629 Evaluate side-chains 158 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 192 ASP Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 210 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 0.0170 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 216 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.192677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135488 restraints weight = 9380.405| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.84 r_work: 0.3447 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9154 Z= 0.186 Angle : 0.547 11.213 12424 Z= 0.275 Chirality : 0.042 0.150 1426 Planarity : 0.004 0.047 1571 Dihedral : 4.447 41.996 1259 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.00 % Allowed : 18.60 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1144 helix: 2.25 (0.27), residues: 375 sheet: 0.24 (0.29), residues: 295 loop : -0.20 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 338 HIS 0.004 0.001 HIS B 91 PHE 0.012 0.001 PHE R 161 TYR 0.010 0.001 TYR E 190 ARG 0.007 0.000 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4003.91 seconds wall clock time: 72 minutes 30.65 seconds (4350.65 seconds total)