Starting phenix.real_space_refine on Sun Apr 7 17:57:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0p_32247/04_2024/7w0p_32247.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0p_32247/04_2024/7w0p_32247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0p_32247/04_2024/7w0p_32247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0p_32247/04_2024/7w0p_32247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0p_32247/04_2024/7w0p_32247.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0p_32247/04_2024/7w0p_32247.pdb" } resolution = 3.16 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2057 atoms to isotropic. 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 5788 2.51 5 N 1541 2.21 5 O 1694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9091 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1813 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 418 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "R" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2337 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "S" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "D" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 128 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 11} Time building chain proxies: 5.13, per 1000 atoms: 0.56 Number of scatterers: 9091 At special positions: 0 Unit cell: (90.48, 118.56, 132.08, 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 1694 8.00 N 1541 7.00 C 5788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.8 seconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 37.9% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.553A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.714A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 216' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.049A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.597A pdb=" N ASN C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 76 Processing helix chain 'R' and resid 29 through 55 removed outlier: 4.245A pdb=" N ALA R 33 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 80 Processing helix chain 'R' and resid 81 through 86 removed outlier: 3.648A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 92 Processing helix chain 'R' and resid 98 through 133 removed outlier: 3.736A pdb=" N CYS R 102 " --> pdb=" O GLY R 98 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG R 133 " --> pdb=" O LEU R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 147 removed outlier: 3.936A pdb=" N GLY R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA R 147 " --> pdb=" O ARG R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 162 Processing helix chain 'R' and resid 163 through 165 No H-bonds generated for 'chain 'R' and resid 163 through 165' Processing helix chain 'R' and resid 190 through 233 removed outlier: 4.159A pdb=" N TRP R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY R 209 " --> pdb=" O SER R 205 " (cutoff:3.500A) Proline residue: R 213 - end of helix removed outlier: 4.276A pdb=" N ARG R 233 " --> pdb=" O ALA R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 274 removed outlier: 4.230A pdb=" N ARG R 241 " --> pdb=" O ILE R 237 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS R 242 " --> pdb=" O GLU R 238 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL R 254 " --> pdb=" O ILE R 250 " (cutoff:3.500A) Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 280 through 310 removed outlier: 3.561A pdb=" N ASP R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE R 286 " --> pdb=" O ASP R 282 " (cutoff:3.500A) Proline residue: R 292 - end of helix removed outlier: 3.893A pdb=" N CYS R 296 " --> pdb=" O PRO R 292 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASN R 301 " --> pdb=" O ILE R 297 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 317 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.557A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'D' and resid 21 through 27 removed outlier: 4.368A pdb=" N HIS D 26 " --> pdb=" O CYS D 21 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.148A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.535A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.773A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.919A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.866A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.200A 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: 6.620A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.526A 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: 3.610A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.843A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 5 through 7 removed outlier: 3.536A pdb=" N SER S 23 " --> pdb=" O VAL S 5 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP S 73 " --> pdb=" O THR S 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 49 through 51 removed outlier: 3.703A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 49 through 51 removed outlier: 3.703A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.852A pdb=" N ASN S 194 " --> pdb=" O ARG S 191 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG S 191 " --> pdb=" O ASN S 194 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU S 178 " --> pdb=" O GLN S 186 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1161 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: 2.55 Time building geometry restraints manager: 3.67 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: 2910 1.34 - 1.46: 1722 1.46 - 1.58: 4556 1.58 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 9288 Sorted by residual: bond pdb=" C ILE R 31 " pdb=" N PRO R 32 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.30e-02 5.92e+03 6.91e+00 bond pdb=" N VAL S 2 " pdb=" CA VAL S 2 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.29e-02 6.01e+03 6.84e+00 bond pdb=" N ASP S 1 " pdb=" CA ASP S 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.56e+00 bond pdb=" CG1 ILE R 250 " pdb=" CD1 ILE R 250 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.46e+00 bond pdb=" CB CYS C 72 " pdb=" SG CYS C 72 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.28e+00 ... (remaining 9283 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.17: 183 106.17 - 113.12: 4985 113.12 - 120.07: 3224 120.07 - 127.02: 4096 127.02 - 133.97: 96 Bond angle restraints: 12584 Sorted by residual: angle pdb=" C ILE R 34 " pdb=" N TYR R 35 " pdb=" CA TYR R 35 " ideal model delta sigma weight residual 121.14 113.90 7.24 1.75e+00 3.27e-01 1.71e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 109.44 3.76 9.60e-01 1.09e+00 1.53e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 128.43 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" C MET R 113 " pdb=" N TYR R 114 " pdb=" CA TYR R 114 " ideal model delta sigma weight residual 120.68 114.97 5.71 1.70e+00 3.46e-01 1.13e+01 angle pdb=" CA MET R 187 " pdb=" CB MET R 187 " pdb=" CG MET R 187 " ideal model delta sigma weight residual 114.10 120.63 -6.53 2.00e+00 2.50e-01 1.07e+01 ... (remaining 12579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 4949 15.46 - 30.92: 437 30.92 - 46.38: 99 46.38 - 61.84: 13 61.84 - 77.30: 2 Dihedral angle restraints: 5500 sinusoidal: 2140 harmonic: 3360 Sorted by residual: dihedral pdb=" CA THR B 164 " pdb=" C THR B 164 " pdb=" N THR B 165 " pdb=" CA THR B 165 " ideal model delta harmonic sigma weight residual -180.00 -155.30 -24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA VAL D 29 " pdb=" C VAL D 29 " pdb=" N PRO D 30 " pdb=" CA PRO D 30 " ideal model delta harmonic sigma weight residual 180.00 -158.08 -21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA TYR S 190 " pdb=" C TYR S 190 " pdb=" N ARG S 191 " pdb=" CA ARG S 191 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 5497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1054 0.044 - 0.088: 276 0.088 - 0.132: 78 0.132 - 0.176: 9 0.176 - 0.220: 4 Chirality restraints: 1421 Sorted by residual: chirality pdb=" CA ASN R 305 " pdb=" N ASN R 305 " pdb=" C ASN R 305 " pdb=" CB ASN R 305 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL S 2 " pdb=" N VAL S 2 " pdb=" C VAL S 2 " pdb=" CB VAL S 2 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE S 58 " pdb=" CA ILE S 58 " pdb=" CG1 ILE S 58 " pdb=" CG2 ILE S 58 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1418 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO S 236 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR S 150 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO S 151 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO S 151 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO S 151 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO B 236 " 0.083 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 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 757 2.74 - 3.28: 9303 3.28 - 3.82: 15004 3.82 - 4.36: 17273 4.36 - 4.90: 30123 Nonbonded interactions: 72460 Sorted by model distance: nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR R 114 " pdb=" O ALA R 157 " model vdw 2.225 2.440 nonbonded pdb=" OG SER B 122 " pdb=" OE2 GLU B 138 " model vdw 2.254 2.440 nonbonded pdb=" ND2 ASN B 237 " pdb=" OD1 ASN B 239 " model vdw 2.280 2.520 ... (remaining 72455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 3.840 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.390 Find NCS groups from input model: 0.260 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9288 Z= 0.216 Angle : 0.652 9.424 12584 Z= 0.350 Chirality : 0.044 0.220 1421 Planarity : 0.004 0.063 1590 Dihedral : 12.424 77.301 3331 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.57 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.24), residues: 1142 helix: 0.85 (0.27), residues: 372 sheet: -0.08 (0.31), residues: 275 loop : -2.21 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 195 HIS 0.003 0.001 HIS B 142 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.001 TYR R 107 ARG 0.013 0.001 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7772 (mptt) cc_final: 0.7254 (mptt) REVERT: A 36 LEU cc_start: 0.7700 (mt) cc_final: 0.7466 (mp) REVERT: A 194 LEU cc_start: 0.7963 (tp) cc_final: 0.7681 (tp) REVERT: A 262 THR cc_start: 0.8384 (m) cc_final: 0.7787 (m) REVERT: A 270 LYS cc_start: 0.7983 (mppt) cc_final: 0.7519 (mppt) REVERT: A 275 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7094 (mt-10) REVERT: A 317 LYS cc_start: 0.7103 (ptmt) cc_final: 0.6852 (ptmt) REVERT: A 321 THR cc_start: 0.8149 (t) cc_final: 0.7907 (t) REVERT: A 333 GLN cc_start: 0.7648 (tp40) cc_final: 0.7073 (tp40) REVERT: A 348 LEU cc_start: 0.8315 (mm) cc_final: 0.8095 (mm) REVERT: A 349 LYS cc_start: 0.8057 (mttm) cc_final: 0.7715 (mttm) REVERT: B 22 ARG cc_start: 0.6723 (ptp-110) cc_final: 0.6486 (ptp-110) REVERT: B 61 MET cc_start: 0.7313 (ppp) cc_final: 0.6766 (ppp) REVERT: B 120 ILE cc_start: 0.8236 (pt) cc_final: 0.8033 (pt) REVERT: B 155 ASN cc_start: 0.7044 (t0) cc_final: 0.6668 (t0) REVERT: B 197 ARG cc_start: 0.6587 (mpt180) cc_final: 0.6367 (mpt180) REVERT: B 228 ASP cc_start: 0.6776 (m-30) cc_final: 0.6542 (m-30) REVERT: B 246 ASP cc_start: 0.6667 (t70) cc_final: 0.6343 (t70) REVERT: B 247 ASP cc_start: 0.6194 (t0) cc_final: 0.5826 (t0) REVERT: B 314 ARG cc_start: 0.6975 (mtp85) cc_final: 0.6699 (mtp85) REVERT: B 325 MET cc_start: 0.6220 (mpp) cc_final: 0.5658 (mpp) REVERT: C 52 MET cc_start: 0.7227 (tpt) cc_final: 0.6803 (tpt) REVERT: R 129 LEU cc_start: 0.7409 (tp) cc_final: 0.7165 (tp) REVERT: R 131 ILE cc_start: 0.8303 (mp) cc_final: 0.8084 (mp) REVERT: R 187 MET cc_start: 0.4502 (pmm) cc_final: 0.3565 (pmm) REVERT: R 289 ASN cc_start: 0.5309 (t0) cc_final: 0.3915 (t0) REVERT: S 57 THR cc_start: 0.7925 (p) cc_final: 0.7721 (p) REVERT: S 118 THR cc_start: 0.7889 (p) cc_final: 0.7643 (p) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2400 time to fit residues: 86.2958 Evaluate side-chains 259 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.0470 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 88 optimal weight: 0.0670 chunk 34 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 304 GLN B 88 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9288 Z= 0.179 Angle : 0.610 7.401 12584 Z= 0.322 Chirality : 0.043 0.208 1421 Planarity : 0.005 0.060 1590 Dihedral : 4.753 25.556 1261 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 0.81 % Allowed : 9.58 % Favored : 89.62 % 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: -0.73 (0.24), residues: 1142 helix: 1.13 (0.27), residues: 376 sheet: 0.20 (0.32), residues: 256 loop : -2.18 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 195 HIS 0.003 0.001 HIS A 188 PHE 0.013 0.001 PHE B 278 TYR 0.046 0.002 TYR R 114 ARG 0.006 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 267 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7783 (mptt) cc_final: 0.7155 (mptt) REVERT: A 194 LEU cc_start: 0.7972 (tp) cc_final: 0.7661 (tp) REVERT: A 262 THR cc_start: 0.8382 (m) cc_final: 0.7923 (m) REVERT: A 270 LYS cc_start: 0.7624 (mppt) cc_final: 0.7160 (mppt) REVERT: A 317 LYS cc_start: 0.7116 (ptmt) cc_final: 0.6910 (ptmt) REVERT: A 333 GLN cc_start: 0.7617 (tp40) cc_final: 0.7031 (tp40) REVERT: A 336 PHE cc_start: 0.7672 (t80) cc_final: 0.7352 (t80) REVERT: A 349 LYS cc_start: 0.8004 (mttm) cc_final: 0.7646 (mttm) REVERT: B 46 ARG cc_start: 0.6422 (ptt-90) cc_final: 0.6153 (ptt-90) REVERT: B 48 ARG cc_start: 0.7150 (mmm160) cc_final: 0.5836 (mmm160) REVERT: B 120 ILE cc_start: 0.8203 (pt) cc_final: 0.7804 (mt) REVERT: B 155 ASN cc_start: 0.7204 (t0) cc_final: 0.6814 (t0) REVERT: B 175 GLN cc_start: 0.6552 (mp10) cc_final: 0.6225 (mp10) REVERT: B 232 ILE cc_start: 0.8132 (mt) cc_final: 0.7862 (tp) REVERT: B 246 ASP cc_start: 0.6657 (t70) cc_final: 0.6384 (t70) REVERT: B 247 ASP cc_start: 0.6316 (t0) cc_final: 0.5866 (t0) REVERT: B 325 MET cc_start: 0.6090 (mpp) cc_final: 0.5746 (mpp) REVERT: C 52 MET cc_start: 0.7205 (tpt) cc_final: 0.6767 (tpt) REVERT: C 61 VAL cc_start: 0.7744 (t) cc_final: 0.7464 (p) REVERT: R 131 ILE cc_start: 0.8304 (mp) cc_final: 0.8006 (mp) REVERT: R 187 MET cc_start: 0.4414 (pmm) cc_final: 0.3688 (pmm) REVERT: R 250 ILE cc_start: 0.7681 (mp) cc_final: 0.7301 (mp) REVERT: R 289 ASN cc_start: 0.5291 (t0) cc_final: 0.4653 (t0) REVERT: R 293 TYR cc_start: 0.6411 (m-80) cc_final: 0.6105 (m-80) REVERT: S 57 THR cc_start: 0.7913 (p) cc_final: 0.7709 (p) REVERT: S 80 PHE cc_start: 0.7819 (m-80) cc_final: 0.7426 (m-80) REVERT: S 95 TYR cc_start: 0.8126 (m-80) cc_final: 0.7851 (m-80) REVERT: S 118 THR cc_start: 0.7805 (p) cc_final: 0.7597 (p) outliers start: 8 outliers final: 6 residues processed: 270 average time/residue: 0.2341 time to fit residues: 84.6764 Evaluate side-chains 269 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 263 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 199 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.0000 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 102 optimal weight: 0.0470 chunk 111 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 132 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9288 Z= 0.191 Angle : 0.589 7.658 12584 Z= 0.310 Chirality : 0.042 0.185 1421 Planarity : 0.004 0.059 1590 Dihedral : 4.756 33.098 1261 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.83 % Favored : 93.08 % Rotamer: Outliers : 2.22 % Allowed : 12.20 % Favored : 85.58 % 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: -0.68 (0.24), residues: 1142 helix: 1.21 (0.27), residues: 376 sheet: 0.12 (0.32), residues: 248 loop : -2.08 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS A 188 PHE 0.017 0.001 PHE S 68 TYR 0.048 0.002 TYR R 114 ARG 0.006 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 265 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7761 (mptt) cc_final: 0.7065 (mptt) REVERT: A 194 LEU cc_start: 0.7949 (tp) cc_final: 0.7628 (tp) REVERT: A 262 THR cc_start: 0.8378 (m) cc_final: 0.8013 (m) REVERT: A 270 LYS cc_start: 0.7610 (mppt) cc_final: 0.7158 (mppt) REVERT: A 271 LYS cc_start: 0.7333 (tttt) cc_final: 0.6981 (mttt) REVERT: A 333 GLN cc_start: 0.7612 (tp40) cc_final: 0.7040 (tp40) REVERT: A 336 PHE cc_start: 0.7718 (t80) cc_final: 0.7397 (t80) REVERT: A 348 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8042 (mm) REVERT: A 349 LYS cc_start: 0.8041 (mttm) cc_final: 0.7684 (mttm) REVERT: B 46 ARG cc_start: 0.6454 (ptt-90) cc_final: 0.6153 (ptt-90) REVERT: B 48 ARG cc_start: 0.7255 (mmm160) cc_final: 0.6030 (mmm160) REVERT: B 120 ILE cc_start: 0.8165 (pt) cc_final: 0.7845 (mt) REVERT: B 155 ASN cc_start: 0.7212 (t0) cc_final: 0.6780 (t0) REVERT: B 175 GLN cc_start: 0.6539 (mp10) cc_final: 0.6201 (mp10) REVERT: B 246 ASP cc_start: 0.6701 (t70) cc_final: 0.6393 (t70) REVERT: B 314 ARG cc_start: 0.6958 (mtp85) cc_final: 0.6753 (mtp85) REVERT: B 325 MET cc_start: 0.6202 (mpp) cc_final: 0.5746 (mpp) REVERT: C 52 MET cc_start: 0.7208 (tpt) cc_final: 0.6792 (tpt) REVERT: R 131 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7983 (mp) REVERT: R 183 MET cc_start: 0.4299 (mtt) cc_final: 0.3996 (mtt) REVERT: R 187 MET cc_start: 0.4202 (pmm) cc_final: 0.3908 (pmm) REVERT: R 246 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6253 (tp) REVERT: R 250 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7319 (mp) REVERT: R 289 ASN cc_start: 0.5300 (t0) cc_final: 0.4367 (t0) REVERT: R 293 TYR cc_start: 0.6450 (m-80) cc_final: 0.6215 (m-80) REVERT: S 80 PHE cc_start: 0.7775 (m-80) cc_final: 0.7428 (m-80) REVERT: S 95 TYR cc_start: 0.8274 (m-80) cc_final: 0.8023 (m-80) outliers start: 22 outliers final: 10 residues processed: 273 average time/residue: 0.2345 time to fit residues: 85.6067 Evaluate side-chains 268 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 254 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 131 ILE Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9288 Z= 0.262 Angle : 0.618 10.779 12584 Z= 0.322 Chirality : 0.044 0.199 1421 Planarity : 0.004 0.058 1590 Dihedral : 4.842 34.178 1261 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.36 % Favored : 92.56 % Rotamer: Outliers : 1.81 % Allowed : 15.42 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1142 helix: 1.22 (0.27), residues: 376 sheet: -0.03 (0.32), residues: 262 loop : -2.11 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS A 213 PHE 0.018 0.002 PHE B 278 TYR 0.044 0.002 TYR R 114 ARG 0.006 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 254 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7813 (mptt) cc_final: 0.7134 (mptt) REVERT: A 194 LEU cc_start: 0.7951 (tp) cc_final: 0.7623 (tp) REVERT: A 270 LYS cc_start: 0.7597 (mppt) cc_final: 0.7176 (mppt) REVERT: A 271 LYS cc_start: 0.7333 (tttt) cc_final: 0.6971 (mttt) REVERT: A 333 GLN cc_start: 0.7652 (tp40) cc_final: 0.7083 (tp40) REVERT: A 336 PHE cc_start: 0.7690 (t80) cc_final: 0.7373 (t80) REVERT: A 348 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8094 (mm) REVERT: A 349 LYS cc_start: 0.8055 (mttm) cc_final: 0.7710 (mttm) REVERT: B 46 ARG cc_start: 0.6524 (ptt-90) cc_final: 0.6254 (ptt-90) REVERT: B 48 ARG cc_start: 0.7338 (mmm160) cc_final: 0.6089 (mmm160) REVERT: B 120 ILE cc_start: 0.8187 (pt) cc_final: 0.7964 (mt) REVERT: B 155 ASN cc_start: 0.7199 (t0) cc_final: 0.6812 (t0) REVERT: B 175 GLN cc_start: 0.6600 (mp10) cc_final: 0.6263 (mp10) REVERT: B 197 ARG cc_start: 0.6547 (mpt180) cc_final: 0.6247 (mpt180) REVERT: B 230 ASN cc_start: 0.7390 (m-40) cc_final: 0.7106 (m110) REVERT: B 246 ASP cc_start: 0.6662 (t70) cc_final: 0.6346 (t70) REVERT: B 291 ASP cc_start: 0.7620 (p0) cc_final: 0.7021 (p0) REVERT: B 293 ASN cc_start: 0.8398 (p0) cc_final: 0.7907 (p0) REVERT: B 323 ASP cc_start: 0.6788 (t0) cc_final: 0.6486 (t0) REVERT: B 325 MET cc_start: 0.6260 (mpp) cc_final: 0.5770 (mpp) REVERT: C 52 MET cc_start: 0.7211 (tpt) cc_final: 0.6820 (tpt) REVERT: R 127 ARG cc_start: 0.6846 (mtt180) cc_final: 0.6379 (mtt180) REVERT: R 131 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7997 (mp) REVERT: R 183 MET cc_start: 0.4209 (mtt) cc_final: 0.3894 (mtt) REVERT: R 187 MET cc_start: 0.5657 (pmm) cc_final: 0.5003 (pmm) REVERT: R 246 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6298 (tp) REVERT: R 250 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7449 (mp) REVERT: R 289 ASN cc_start: 0.5381 (t0) cc_final: 0.4282 (t0) REVERT: R 293 TYR cc_start: 0.6488 (m-80) cc_final: 0.6251 (m-80) REVERT: S 80 PHE cc_start: 0.7760 (m-80) cc_final: 0.7435 (m-80) REVERT: S 90 ASP cc_start: 0.7577 (m-30) cc_final: 0.7371 (t0) outliers start: 18 outliers final: 8 residues processed: 262 average time/residue: 0.2498 time to fit residues: 86.5446 Evaluate side-chains 263 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 251 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 131 ILE Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.0270 chunk 93 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 132 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9288 Z= 0.205 Angle : 0.590 8.112 12584 Z= 0.309 Chirality : 0.042 0.188 1421 Planarity : 0.004 0.057 1590 Dihedral : 4.749 34.163 1261 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 2.02 % Allowed : 17.24 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1142 helix: 1.32 (0.27), residues: 376 sheet: -0.09 (0.32), residues: 252 loop : -2.07 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS A 188 PHE 0.017 0.001 PHE A 274 TYR 0.048 0.002 TYR R 114 ARG 0.005 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 254 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7810 (mptt) cc_final: 0.7109 (mptt) REVERT: A 194 LEU cc_start: 0.7952 (tp) cc_final: 0.7614 (tp) REVERT: A 270 LYS cc_start: 0.7557 (mppt) cc_final: 0.7116 (mppt) REVERT: A 271 LYS cc_start: 0.7299 (tttt) cc_final: 0.6968 (mttt) REVERT: A 333 GLN cc_start: 0.7654 (tp40) cc_final: 0.7073 (tp40) REVERT: A 336 PHE cc_start: 0.7676 (t80) cc_final: 0.7340 (t80) REVERT: A 348 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8043 (mm) REVERT: A 349 LYS cc_start: 0.8025 (mttm) cc_final: 0.7685 (mttm) REVERT: B 155 ASN cc_start: 0.7198 (t0) cc_final: 0.6837 (t0) REVERT: B 175 GLN cc_start: 0.6554 (mp10) cc_final: 0.6212 (mp10) REVERT: B 230 ASN cc_start: 0.7387 (m-40) cc_final: 0.7108 (m110) REVERT: B 232 ILE cc_start: 0.8150 (mt) cc_final: 0.7935 (tp) REVERT: B 246 ASP cc_start: 0.6649 (t70) cc_final: 0.6327 (t70) REVERT: B 323 ASP cc_start: 0.6698 (t0) cc_final: 0.6449 (t0) REVERT: B 325 MET cc_start: 0.6272 (mpp) cc_final: 0.5783 (mpp) REVERT: C 52 MET cc_start: 0.7217 (tpt) cc_final: 0.6814 (tpt) REVERT: R 127 ARG cc_start: 0.6794 (mtt180) cc_final: 0.6315 (mtt180) REVERT: R 131 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7993 (mp) REVERT: R 165 MET cc_start: 0.2766 (mmm) cc_final: 0.2533 (mmm) REVERT: R 183 MET cc_start: 0.4266 (mtt) cc_final: 0.3933 (mtt) REVERT: R 187 MET cc_start: 0.5246 (pmm) cc_final: 0.4542 (pmm) REVERT: R 246 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6278 (tp) REVERT: R 250 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7448 (mp) REVERT: R 289 ASN cc_start: 0.5334 (t0) cc_final: 0.4242 (t0) REVERT: S 80 PHE cc_start: 0.7714 (m-80) cc_final: 0.7372 (m-80) REVERT: S 90 ASP cc_start: 0.7554 (m-30) cc_final: 0.7334 (t0) outliers start: 20 outliers final: 11 residues processed: 264 average time/residue: 0.2520 time to fit residues: 88.0934 Evaluate side-chains 266 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 251 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 131 ILE Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9288 Z= 0.241 Angle : 0.610 8.594 12584 Z= 0.319 Chirality : 0.043 0.204 1421 Planarity : 0.004 0.057 1590 Dihedral : 4.821 34.655 1261 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.82 % Rotamer: Outliers : 2.02 % Allowed : 18.04 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.72 (0.25), residues: 1142 helix: 1.31 (0.27), residues: 376 sheet: -0.18 (0.33), residues: 254 loop : -2.08 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS A 188 PHE 0.016 0.001 PHE B 278 TYR 0.049 0.002 TYR R 114 ARG 0.005 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 249 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7769 (mptt) cc_final: 0.7078 (mptt) REVERT: A 194 LEU cc_start: 0.7952 (tp) cc_final: 0.7619 (tp) REVERT: A 270 LYS cc_start: 0.7576 (mppt) cc_final: 0.7142 (mppt) REVERT: A 271 LYS cc_start: 0.7313 (tttt) cc_final: 0.7037 (mttt) REVERT: A 333 GLN cc_start: 0.7655 (tp40) cc_final: 0.7087 (tp40) REVERT: A 336 PHE cc_start: 0.7661 (t80) cc_final: 0.7349 (t80) REVERT: A 348 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8063 (mm) REVERT: A 349 LYS cc_start: 0.8030 (mttm) cc_final: 0.7692 (mttm) REVERT: B 97 SER cc_start: 0.8157 (t) cc_final: 0.7839 (p) REVERT: B 143 THR cc_start: 0.8065 (t) cc_final: 0.7835 (p) REVERT: B 155 ASN cc_start: 0.7210 (t0) cc_final: 0.6803 (t0) REVERT: B 175 GLN cc_start: 0.6581 (mp10) cc_final: 0.6236 (mp10) REVERT: B 232 ILE cc_start: 0.8132 (mt) cc_final: 0.7918 (tp) REVERT: B 246 ASP cc_start: 0.6658 (t70) cc_final: 0.6356 (t70) REVERT: B 293 ASN cc_start: 0.8489 (p0) cc_final: 0.8098 (p0) REVERT: B 323 ASP cc_start: 0.6722 (t0) cc_final: 0.6378 (t0) REVERT: B 325 MET cc_start: 0.6340 (mpp) cc_final: 0.5726 (mpp) REVERT: C 52 MET cc_start: 0.7227 (tpt) cc_final: 0.6817 (tpt) REVERT: R 127 ARG cc_start: 0.6817 (mtt180) cc_final: 0.6339 (mtt180) REVERT: R 131 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7973 (mp) REVERT: R 183 MET cc_start: 0.4304 (mtt) cc_final: 0.3970 (mtt) REVERT: R 187 MET cc_start: 0.5541 (pmm) cc_final: 0.4799 (pmm) REVERT: R 246 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6295 (tp) REVERT: R 250 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7452 (mp) REVERT: S 80 PHE cc_start: 0.7737 (m-80) cc_final: 0.7368 (m-80) REVERT: S 90 ASP cc_start: 0.7560 (m-30) cc_final: 0.7359 (t0) outliers start: 20 outliers final: 13 residues processed: 258 average time/residue: 0.2497 time to fit residues: 85.4660 Evaluate side-chains 265 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 248 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 131 ILE Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 305 ASN Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 40.0000 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9288 Z= 0.221 Angle : 0.604 8.665 12584 Z= 0.318 Chirality : 0.043 0.198 1421 Planarity : 0.005 0.057 1590 Dihedral : 4.791 34.757 1261 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 2.62 % Allowed : 18.45 % 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: -0.69 (0.25), residues: 1142 helix: 1.35 (0.27), residues: 376 sheet: -0.11 (0.33), residues: 252 loop : -2.10 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS A 188 PHE 0.016 0.001 PHE R 39 TYR 0.048 0.002 TYR R 114 ARG 0.007 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 248 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7761 (mptt) cc_final: 0.7064 (mptt) REVERT: A 194 LEU cc_start: 0.7948 (tp) cc_final: 0.7633 (tp) REVERT: A 270 LYS cc_start: 0.7574 (mppt) cc_final: 0.7128 (mppt) REVERT: A 271 LYS cc_start: 0.7324 (tttt) cc_final: 0.7048 (mttt) REVERT: A 333 GLN cc_start: 0.7660 (tp40) cc_final: 0.7093 (tp40) REVERT: A 348 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8063 (mm) REVERT: A 349 LYS cc_start: 0.8030 (mttm) cc_final: 0.7685 (mttm) REVERT: B 97 SER cc_start: 0.8150 (t) cc_final: 0.7827 (p) REVERT: B 143 THR cc_start: 0.8084 (t) cc_final: 0.7876 (p) REVERT: B 155 ASN cc_start: 0.7246 (t0) cc_final: 0.6845 (t0) REVERT: B 175 GLN cc_start: 0.6562 (mp10) cc_final: 0.6210 (mp10) REVERT: B 230 ASN cc_start: 0.7331 (m-40) cc_final: 0.7041 (m110) REVERT: B 232 ILE cc_start: 0.8136 (mt) cc_final: 0.7923 (tp) REVERT: B 293 ASN cc_start: 0.8438 (p0) cc_final: 0.8061 (p0) REVERT: B 325 MET cc_start: 0.6359 (mpp) cc_final: 0.5769 (mpp) REVERT: C 52 MET cc_start: 0.7228 (tpt) cc_final: 0.6818 (tpt) REVERT: R 127 ARG cc_start: 0.6815 (mtt180) cc_final: 0.6336 (mtt180) REVERT: R 131 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7971 (mp) REVERT: R 183 MET cc_start: 0.4399 (mtt) cc_final: 0.4040 (mtt) REVERT: R 187 MET cc_start: 0.5583 (OUTLIER) cc_final: 0.4868 (pmm) REVERT: R 246 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6290 (tp) REVERT: R 250 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7445 (mp) REVERT: S 80 PHE cc_start: 0.7739 (m-80) cc_final: 0.7350 (m-80) outliers start: 26 outliers final: 15 residues processed: 261 average time/residue: 0.2455 time to fit residues: 84.7003 Evaluate side-chains 269 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 249 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 131 ILE Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 305 ASN Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.0050 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 85 optimal weight: 0.0470 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 95 optimal weight: 0.0070 overall best weight: 0.3310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9288 Z= 0.176 Angle : 0.616 9.659 12584 Z= 0.321 Chirality : 0.043 0.197 1421 Planarity : 0.005 0.056 1590 Dihedral : 4.728 33.810 1261 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.01 % Favored : 92.91 % Rotamer: Outliers : 2.42 % Allowed : 18.95 % Favored : 78.63 % 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: -0.62 (0.25), residues: 1142 helix: 1.44 (0.27), residues: 376 sheet: -0.01 (0.33), residues: 247 loop : -2.11 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.003 0.001 HIS A 188 PHE 0.038 0.001 PHE A 336 TYR 0.048 0.002 TYR R 114 ARG 0.007 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 247 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7719 (mptt) cc_final: 0.7021 (mptt) REVERT: A 194 LEU cc_start: 0.7943 (tp) cc_final: 0.7667 (tp) REVERT: A 243 MET cc_start: 0.7003 (tpp) cc_final: 0.6759 (tpp) REVERT: A 270 LYS cc_start: 0.7544 (mppt) cc_final: 0.7106 (mppt) REVERT: A 271 LYS cc_start: 0.7320 (tttt) cc_final: 0.7030 (mttt) REVERT: A 274 PHE cc_start: 0.7868 (t80) cc_final: 0.7262 (t80) REVERT: A 333 GLN cc_start: 0.7665 (tp40) cc_final: 0.7059 (tp40) REVERT: A 348 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8062 (mm) REVERT: A 349 LYS cc_start: 0.8013 (mttm) cc_final: 0.7669 (mttm) REVERT: B 32 GLN cc_start: 0.7165 (tp40) cc_final: 0.6864 (tp40) REVERT: B 155 ASN cc_start: 0.7250 (t0) cc_final: 0.6864 (t0) REVERT: B 175 GLN cc_start: 0.6384 (mp10) cc_final: 0.6019 (mp10) REVERT: B 293 ASN cc_start: 0.8441 (p0) cc_final: 0.8063 (p0) REVERT: B 325 MET cc_start: 0.6191 (mpp) cc_final: 0.5827 (mpp) REVERT: C 52 MET cc_start: 0.7214 (tpt) cc_final: 0.6811 (tpt) REVERT: R 127 ARG cc_start: 0.6761 (mtt180) cc_final: 0.6293 (mtt180) REVERT: R 131 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7977 (mp) REVERT: R 183 MET cc_start: 0.4361 (mtt) cc_final: 0.4006 (mtt) REVERT: R 187 MET cc_start: 0.5568 (OUTLIER) cc_final: 0.4862 (pmm) REVERT: R 246 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6253 (tp) REVERT: R 250 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7431 (mp) REVERT: S 80 PHE cc_start: 0.7658 (m-80) cc_final: 0.7301 (m-80) outliers start: 24 outliers final: 16 residues processed: 259 average time/residue: 0.2474 time to fit residues: 84.7916 Evaluate side-chains 262 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 241 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 131 ILE Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 305 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 233 LEU 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: 0.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.0980 chunk 79 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 0.0060 chunk 65 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9288 Z= 0.192 Angle : 0.614 9.127 12584 Z= 0.323 Chirality : 0.043 0.198 1421 Planarity : 0.005 0.056 1590 Dihedral : 4.758 34.230 1261 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.01 % Favored : 92.91 % Rotamer: Outliers : 2.22 % Allowed : 19.86 % Favored : 77.92 % 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: -0.60 (0.25), residues: 1142 helix: 1.46 (0.27), residues: 376 sheet: 0.02 (0.33), residues: 247 loop : -2.12 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.003 0.001 HIS A 188 PHE 0.032 0.001 PHE A 336 TYR 0.047 0.002 TYR R 114 ARG 0.006 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.7943 (tp) cc_final: 0.7664 (tp) REVERT: A 243 MET cc_start: 0.7017 (tpp) cc_final: 0.6771 (tpp) REVERT: A 270 LYS cc_start: 0.7549 (mppt) cc_final: 0.7109 (mppt) REVERT: A 271 LYS cc_start: 0.7319 (tttt) cc_final: 0.7052 (mttt) REVERT: A 333 GLN cc_start: 0.7664 (tp40) cc_final: 0.7070 (tp40) REVERT: A 348 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8081 (mm) REVERT: A 349 LYS cc_start: 0.8036 (mttm) cc_final: 0.7688 (mttm) REVERT: B 32 GLN cc_start: 0.7198 (tp40) cc_final: 0.6879 (tp40) REVERT: B 155 ASN cc_start: 0.7253 (t0) cc_final: 0.6859 (t0) REVERT: B 175 GLN cc_start: 0.6396 (mp10) cc_final: 0.6030 (mp10) REVERT: B 293 ASN cc_start: 0.8430 (p0) cc_final: 0.8065 (p0) REVERT: B 325 MET cc_start: 0.6242 (mpp) cc_final: 0.5857 (mpp) REVERT: C 52 MET cc_start: 0.7215 (tpt) cc_final: 0.6804 (tpt) REVERT: R 127 ARG cc_start: 0.6788 (mtt180) cc_final: 0.6290 (mtt180) REVERT: R 131 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7974 (mp) REVERT: R 183 MET cc_start: 0.4348 (mtt) cc_final: 0.4002 (mtt) REVERT: R 187 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.4907 (pmm) REVERT: R 246 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6256 (tp) REVERT: R 250 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7434 (mp) REVERT: S 80 PHE cc_start: 0.7645 (m-80) cc_final: 0.7270 (m-80) REVERT: S 99 SER cc_start: 0.8225 (p) cc_final: 0.7991 (p) outliers start: 22 outliers final: 14 residues processed: 257 average time/residue: 0.2491 time to fit residues: 84.8478 Evaluate side-chains 263 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 244 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 131 ILE Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 305 ASN Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 112 optimal weight: 0.0270 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 0.0070 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 71 optimal weight: 50.0000 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9288 Z= 0.188 Angle : 0.620 9.222 12584 Z= 0.325 Chirality : 0.043 0.206 1421 Planarity : 0.005 0.061 1590 Dihedral : 4.767 34.040 1261 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 2.12 % Allowed : 19.96 % Favored : 77.92 % 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: -0.59 (0.25), residues: 1142 helix: 1.46 (0.27), residues: 376 sheet: 0.04 (0.33), residues: 248 loop : -2.11 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS A 188 PHE 0.030 0.001 PHE A 336 TYR 0.045 0.002 TYR R 114 ARG 0.006 0.000 ARG B 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 241 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.5567 (mmm) cc_final: 0.5364 (mmm) REVERT: A 192 LYS cc_start: 0.8033 (mttp) cc_final: 0.7772 (mttp) REVERT: A 194 LEU cc_start: 0.7941 (tp) cc_final: 0.7666 (tp) REVERT: A 243 MET cc_start: 0.7018 (tpp) cc_final: 0.6773 (tpp) REVERT: A 270 LYS cc_start: 0.7539 (mppt) cc_final: 0.7094 (mppt) REVERT: A 271 LYS cc_start: 0.7306 (tttt) cc_final: 0.6979 (mttt) REVERT: A 274 PHE cc_start: 0.7846 (t80) cc_final: 0.7284 (t80) REVERT: A 333 GLN cc_start: 0.7663 (tp40) cc_final: 0.7104 (tp40) REVERT: A 348 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8077 (mm) REVERT: A 349 LYS cc_start: 0.8036 (mttm) cc_final: 0.7686 (mttm) REVERT: B 32 GLN cc_start: 0.7114 (tp40) cc_final: 0.6803 (tp40) REVERT: B 155 ASN cc_start: 0.7254 (t0) cc_final: 0.6869 (t0) REVERT: B 175 GLN cc_start: 0.6294 (mp10) cc_final: 0.5938 (mp10) REVERT: B 230 ASN cc_start: 0.7282 (m-40) cc_final: 0.6955 (m110) REVERT: B 251 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7775 (mtm-85) REVERT: B 293 ASN cc_start: 0.8419 (p0) cc_final: 0.8053 (p0) REVERT: B 325 MET cc_start: 0.6229 (mpp) cc_final: 0.5854 (mpp) REVERT: C 52 MET cc_start: 0.7214 (tpt) cc_final: 0.6808 (tpt) REVERT: R 127 ARG cc_start: 0.6780 (mtt180) cc_final: 0.6285 (mtt180) REVERT: R 131 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7975 (mp) REVERT: R 183 MET cc_start: 0.4382 (mtt) cc_final: 0.3999 (mtt) REVERT: R 187 MET cc_start: 0.5641 (OUTLIER) cc_final: 0.4935 (pmm) REVERT: R 246 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6246 (tp) REVERT: R 250 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7435 (mp) REVERT: S 80 PHE cc_start: 0.7626 (m-80) cc_final: 0.7264 (m-80) REVERT: S 101 TYR cc_start: 0.7913 (m-80) cc_final: 0.7310 (m-80) outliers start: 21 outliers final: 15 residues processed: 252 average time/residue: 0.2468 time to fit residues: 82.4354 Evaluate side-chains 262 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 242 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 131 ILE Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 305 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.0670 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 0.0670 chunk 5 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.192890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.164505 restraints weight = 13722.067| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.84 r_work: 0.3913 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9288 Z= 0.164 Angle : 0.616 9.147 12584 Z= 0.322 Chirality : 0.043 0.214 1421 Planarity : 0.005 0.060 1590 Dihedral : 4.696 33.975 1261 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.18 % Favored : 92.73 % Rotamer: Outliers : 2.02 % Allowed : 19.96 % Favored : 78.02 % 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: -0.55 (0.25), residues: 1142 helix: 1.49 (0.27), residues: 378 sheet: 0.08 (0.34), residues: 248 loop : -2.10 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.003 0.001 HIS A 188 PHE 0.028 0.001 PHE A 336 TYR 0.045 0.002 TYR R 114 ARG 0.007 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2662.28 seconds wall clock time: 49 minutes 8.47 seconds (2948.47 seconds total)