Starting phenix.real_space_refine on Sat Aug 23 00:06:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwh_37888/08_2025/8wwh_37888.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwh_37888/08_2025/8wwh_37888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wwh_37888/08_2025/8wwh_37888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwh_37888/08_2025/8wwh_37888.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wwh_37888/08_2025/8wwh_37888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwh_37888/08_2025/8wwh_37888.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.072 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 64 5.16 5 C 5618 2.51 5 N 1491 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8821 Number of models: 1 Model: "" Number of chains: 5 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: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2235 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 1.64, per 1000 atoms: 0.19 Number of scatterers: 8821 At special positions: 0 Unit cell: (88.81, 116.63, 123.05, 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 64 16.00 O 1648 8.00 N 1491 7.00 C 5618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, 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 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: 0.43 Conformation dependent library (CDL) restraints added in 405.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 38.8% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.503A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.101A 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: 4.002A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.607A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.946A 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 310 removed outlier: 4.295A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.509A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (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 removed outlier: 3.542A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 138 Proline residue: R 113 - end of helix Processing helix chain 'R' and resid 145 through 164 Processing helix chain 'R' and resid 165 through 170 Processing helix chain 'R' and resid 180 through 216 removed outlier: 4.004A pdb=" N MET R 184 " --> pdb=" O PHE R 180 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR R 186 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU R 187 " --> pdb=" O THR R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 223 removed outlier: 3.581A pdb=" N THR R 221 " --> pdb=" O ILE R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 244 Processing helix chain 'R' and resid 244 through 250 removed outlier: 3.517A pdb=" N TRP R 248 " --> pdb=" O ILE R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 286 removed outlier: 3.637A pdb=" N LEU R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N TYR R 275 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TRP R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 303 Processing helix chain 'R' and resid 313 through 351 Proline residue: R 340 - end of helix removed outlier: 3.901A pdb=" N LEU R 349 " --> pdb=" O GLN R 345 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 355 through 384 removed outlier: 4.229A 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 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.242A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.593A 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: 5.767A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.562A 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: 3.593A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.899A 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: 5.973A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.067A 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: 6.233A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.629A 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: 6.921A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.334A 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: 6.482A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.885A 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: 3.686A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.151A 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: 6.809A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.478A 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: 4.257A 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: 6.170A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 253 through 255 removed outlier: 3.651A pdb=" N GLY R 262 " --> pdb=" O ILE R 254 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1299 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: 0.88 Time building geometry restraints manager: 0.63 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: 2844 1.34 - 1.46: 2035 1.46 - 1.58: 4038 1.58 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 9010 Sorted by residual: bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.66e-01 bond pdb=" CG LEU B 318 " pdb=" CD2 LEU B 318 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.84e-01 bond pdb=" CB ASP A 20 " pdb=" CG ASP A 20 " ideal model delta sigma weight residual 1.516 1.497 0.019 2.50e-02 1.60e+03 5.73e-01 bond pdb=" CG1 ILE B 81 " pdb=" CD1 ILE B 81 " ideal model delta sigma weight residual 1.513 1.485 0.028 3.90e-02 6.57e+02 5.11e-01 bond pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 1.513 1.488 0.025 3.90e-02 6.57e+02 4.14e-01 ... (remaining 9005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 11872 1.02 - 2.03: 292 2.03 - 3.05: 52 3.05 - 4.07: 7 4.07 - 5.09: 10 Bond angle restraints: 12233 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 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.42e+00 angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" C MET E 192 " ideal model delta sigma weight residual 110.80 114.53 -3.73 2.13e+00 2.20e-01 3.06e+00 angle pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" C TYR E 102 " ideal model delta sigma weight residual 108.96 106.52 2.44 1.49e+00 4.50e-01 2.67e+00 angle pdb=" CA LEU B 318 " pdb=" CB LEU B 318 " pdb=" CG LEU B 318 " ideal model delta sigma weight residual 116.30 121.39 -5.09 3.50e+00 8.16e-02 2.11e+00 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 123.93 126.11 -2.18 1.54e+00 4.22e-01 2.01e+00 ... (remaining 12228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.72: 4984 11.72 - 23.44: 267 23.44 - 35.17: 58 35.17 - 46.89: 18 46.89 - 58.61: 4 Dihedral angle restraints: 5331 sinusoidal: 2014 harmonic: 3317 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 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.39 18.61 0 5.00e+00 4.00e-02 1.39e+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 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 835 0.028 - 0.056: 359 0.056 - 0.084: 112 0.084 - 0.112: 80 0.112 - 0.140: 20 Chirality restraints: 1406 Sorted by residual: 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 -0.14 2.00e-01 2.50e+01 4.90e-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 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1403 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO B 236 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO E 107 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS R 216 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO R 217 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO R 217 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 217 " -0.014 5.00e-02 4.00e+02 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 221 2.70 - 3.25: 8621 3.25 - 3.80: 14364 3.80 - 4.35: 19363 4.35 - 4.90: 32441 Nonbonded interactions: 75010 Sorted by model distance: nonbonded pdb=" O SER R 243 " pdb=" OH TYR R 280 " model vdw 2.156 3.040 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.253 3.040 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.263 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.273 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.285 3.040 ... (remaining 75005 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: 0.510 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.550 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:5.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 0.036 9013 Z= 0.130 Angle : 0.421 5.087 12239 Z= 0.223 Chirality : 0.041 0.140 1406 Planarity : 0.003 0.046 1547 Dihedral : 8.125 58.611 3182 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.63 % Allowed : 2.42 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.25), residues: 1129 helix: 1.05 (0.26), residues: 399 sheet: 0.78 (0.29), residues: 283 loop : 0.26 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 325 TYR 0.009 0.001 TYR R 280 PHE 0.010 0.001 PHE A 196 TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9010) covalent geometry : angle 0.42072 (12233) SS BOND : bond 0.00086 ( 3) SS BOND : angle 0.73772 ( 6) hydrogen bonds : bond 0.23411 ( 459) hydrogen bonds : angle 7.39105 ( 1299) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 186 time to evaluate : 0.191 Fit side-chains REVERT: A 29 LYS cc_start: 0.8323 (tttt) cc_final: 0.7971 (ttmm) REVERT: A 186 GLU cc_start: 0.8163 (tt0) cc_final: 0.7792 (tt0) REVERT: A 197 LYS cc_start: 0.8119 (mttt) cc_final: 0.7898 (mtpt) REVERT: A 208 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7756 (ttp80) REVERT: A 209 LYS cc_start: 0.8466 (pttt) cc_final: 0.8244 (ptmt) REVERT: A 251 ASP cc_start: 0.8280 (t70) cc_final: 0.8066 (t0) REVERT: A 309 ASP cc_start: 0.7741 (t70) cc_final: 0.7482 (t0) REVERT: A 330 LYS cc_start: 0.7586 (mttt) cc_final: 0.7027 (mtpt) REVERT: B 46 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7400 (mmt-90) REVERT: B 129 ARG cc_start: 0.8078 (mtp180) cc_final: 0.7531 (mmt180) REVERT: C 21 MET cc_start: 0.8460 (mmm) cc_final: 0.7499 (ttt) REVERT: E 43 LYS cc_start: 0.8434 (mmtm) cc_final: 0.8116 (mptp) REVERT: R 148 ASP cc_start: 0.7806 (m-30) cc_final: 0.7534 (m-30) REVERT: R 165 MET cc_start: 0.8601 (ttm) cc_final: 0.7922 (tmm) REVERT: R 191 MET cc_start: 0.7631 (tpt) cc_final: 0.7377 (ttt) REVERT: R 211 TYR cc_start: 0.8489 (t80) cc_final: 0.8183 (t80) REVERT: R 274 LEU cc_start: 0.7266 (tp) cc_final: 0.7020 (tp) REVERT: R 313 GLN cc_start: 0.7252 (tt0) cc_final: 0.6860 (mt0) outliers start: 6 outliers final: 2 residues processed: 189 average time/residue: 0.4900 time to fit residues: 97.9123 Evaluate side-chains 137 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 280 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 30.0000 chunk 106 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** A 204 GLN A 255 ASN A 269 ASN A 322 HIS B 91 HIS R 127 ASN R 196 GLN R 281 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.169973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117306 restraints weight = 10035.351| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.98 r_work: 0.3195 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9013 Z= 0.137 Angle : 0.515 9.597 12239 Z= 0.278 Chirality : 0.042 0.152 1406 Planarity : 0.004 0.058 1547 Dihedral : 4.360 55.795 1236 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.73 % Allowed : 9.35 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.25), residues: 1129 helix: 2.04 (0.26), residues: 403 sheet: 0.86 (0.30), residues: 278 loop : 0.32 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 160 TYR 0.015 0.001 TYR E 190 PHE 0.018 0.001 PHE R 116 TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9010) covalent geometry : angle 0.51499 (12233) SS BOND : bond 0.00278 ( 3) SS BOND : angle 0.90462 ( 6) hydrogen bonds : bond 0.05080 ( 459) hydrogen bonds : angle 4.97862 ( 1299) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.278 Fit side-chains REVERT: A 29 LYS cc_start: 0.8561 (tttt) cc_final: 0.8114 (ttmm) REVERT: A 186 GLU cc_start: 0.8355 (tt0) cc_final: 0.7945 (tt0) REVERT: A 208 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7707 (ttp80) REVERT: A 209 LYS cc_start: 0.8569 (pttt) cc_final: 0.8282 (ptmt) REVERT: A 309 ASP cc_start: 0.7958 (t70) cc_final: 0.7669 (t0) REVERT: A 330 LYS cc_start: 0.7734 (mttt) cc_final: 0.7139 (mtpt) REVERT: B 19 ARG cc_start: 0.6984 (ttp80) cc_final: 0.6553 (ttm110) REVERT: B 46 ARG cc_start: 0.8140 (mtp-110) cc_final: 0.7502 (mmt-90) REVERT: B 129 ARG cc_start: 0.8316 (mtp180) cc_final: 0.7769 (mmt180) REVERT: B 226 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8176 (mp0) REVERT: C 21 MET cc_start: 0.8690 (mmm) cc_final: 0.7955 (ttt) REVERT: C 38 MET cc_start: 0.7730 (ttp) cc_final: 0.7524 (ttp) REVERT: C 46 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7999 (pttp) REVERT: E 43 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8280 (mptp) REVERT: E 77 ASN cc_start: 0.8528 (m-40) cc_final: 0.8294 (m-40) REVERT: E 223 ASP cc_start: 0.7785 (m-30) cc_final: 0.7583 (m-30) REVERT: R 165 MET cc_start: 0.8592 (ttm) cc_final: 0.7982 (tmm) REVERT: R 173 MET cc_start: 0.6975 (tmm) cc_final: 0.6365 (tpt) REVERT: R 313 GLN cc_start: 0.7344 (tt0) cc_final: 0.6953 (mt0) outliers start: 26 outliers final: 11 residues processed: 166 average time/residue: 0.5248 time to fit residues: 92.0615 Evaluate side-chains 148 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 246 ASP 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 154 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 245 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 269 ASN R 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.169814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.117345 restraints weight = 10020.095| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.06 r_work: 0.3223 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9013 Z= 0.146 Angle : 0.504 9.489 12239 Z= 0.268 Chirality : 0.042 0.148 1406 Planarity : 0.004 0.052 1547 Dihedral : 4.034 31.591 1232 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.63 % Allowed : 11.87 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.25), residues: 1129 helix: 2.32 (0.26), residues: 401 sheet: 0.68 (0.29), residues: 290 loop : 0.36 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 160 TYR 0.018 0.001 TYR R 280 PHE 0.012 0.001 PHE A 196 TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9010) covalent geometry : angle 0.50385 (12233) SS BOND : bond 0.00352 ( 3) SS BOND : angle 0.92406 ( 6) hydrogen bonds : bond 0.04388 ( 459) hydrogen bonds : angle 4.77881 ( 1299) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8397 (tttt) cc_final: 0.7878 (ttmm) REVERT: A 186 GLU cc_start: 0.8391 (tt0) cc_final: 0.7822 (tt0) REVERT: A 208 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7516 (ttp80) REVERT: A 209 LYS cc_start: 0.8516 (pttt) cc_final: 0.8171 (ptmt) REVERT: A 255 ASN cc_start: 0.8508 (m-40) cc_final: 0.8271 (m110) REVERT: A 309 ASP cc_start: 0.7954 (t70) cc_final: 0.7661 (t0) REVERT: A 330 LYS cc_start: 0.7678 (mttt) cc_final: 0.7069 (mtpt) REVERT: B 19 ARG cc_start: 0.7030 (ttp80) cc_final: 0.6641 (ttm110) REVERT: B 46 ARG cc_start: 0.8013 (mtp-110) cc_final: 0.7283 (mmt-90) REVERT: B 129 ARG cc_start: 0.8275 (mtp180) cc_final: 0.7670 (mmt180) REVERT: B 226 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8100 (mp0) REVERT: C 21 MET cc_start: 0.8746 (mmm) cc_final: 0.7901 (ttt) REVERT: C 46 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7895 (pttp) REVERT: E 77 ASN cc_start: 0.8519 (m-40) cc_final: 0.8283 (m-40) REVERT: E 145 SER cc_start: 0.8258 (m) cc_final: 0.7924 (p) REVERT: E 223 ASP cc_start: 0.7981 (m-30) cc_final: 0.7692 (m-30) REVERT: R 165 MET cc_start: 0.8688 (ttm) cc_final: 0.8458 (ttp) REVERT: R 173 MET cc_start: 0.7135 (tmm) cc_final: 0.6007 (tpt) REVERT: R 283 PHE cc_start: 0.7398 (t80) cc_final: 0.7142 (m-10) REVERT: R 313 GLN cc_start: 0.7187 (tt0) cc_final: 0.6788 (mt0) REVERT: R 387 PHE cc_start: 0.7822 (t80) cc_final: 0.7567 (t80) outliers start: 25 outliers final: 14 residues processed: 158 average time/residue: 0.5063 time to fit residues: 84.7161 Evaluate side-chains 155 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 chunk 13 optimal weight: 0.3980 chunk 89 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.0944 ------------------------------------------------------------------------------- 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** A 204 GLN A 269 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.169417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116959 restraints weight = 10222.432| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.07 r_work: 0.3210 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9013 Z= 0.140 Angle : 0.502 10.865 12239 Z= 0.263 Chirality : 0.042 0.146 1406 Planarity : 0.004 0.049 1547 Dihedral : 4.041 33.459 1232 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.52 % Allowed : 13.13 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.25), residues: 1129 helix: 2.38 (0.26), residues: 403 sheet: 0.65 (0.30), residues: 277 loop : 0.35 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 160 TYR 0.015 0.001 TYR R 280 PHE 0.013 0.001 PHE R 116 TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9010) covalent geometry : angle 0.50186 (12233) SS BOND : bond 0.00279 ( 3) SS BOND : angle 0.88978 ( 6) hydrogen bonds : bond 0.03987 ( 459) hydrogen bonds : angle 4.64971 ( 1299) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.237 Fit side-chains REVERT: A 29 LYS cc_start: 0.8338 (tttt) cc_final: 0.7820 (ttmm) REVERT: A 186 GLU cc_start: 0.8380 (tt0) cc_final: 0.7631 (tt0) REVERT: A 197 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8075 (mtpp) REVERT: A 208 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7504 (ttp80) REVERT: A 209 LYS cc_start: 0.8481 (pttt) cc_final: 0.8154 (ptmt) REVERT: A 255 ASN cc_start: 0.8494 (m-40) cc_final: 0.8240 (m110) REVERT: A 309 ASP cc_start: 0.7929 (t70) cc_final: 0.7628 (t0) REVERT: A 330 LYS cc_start: 0.7666 (mttt) cc_final: 0.7050 (mtpt) REVERT: B 19 ARG cc_start: 0.7025 (ttp80) cc_final: 0.6652 (ttm110) REVERT: B 46 ARG cc_start: 0.8059 (mtp-110) cc_final: 0.7313 (mmt-90) REVERT: B 129 ARG cc_start: 0.8311 (mtp180) cc_final: 0.7725 (mmt180) REVERT: B 226 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8161 (mp0) REVERT: B 262 MET cc_start: 0.8610 (tpp) cc_final: 0.8332 (tpp) REVERT: C 21 MET cc_start: 0.8749 (mmm) cc_final: 0.7881 (ttt) REVERT: C 46 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7831 (pttp) REVERT: E 43 LYS cc_start: 0.8124 (mptm) cc_final: 0.7819 (mptt) REVERT: E 77 ASN cc_start: 0.8555 (m-40) cc_final: 0.8315 (m-40) REVERT: E 145 SER cc_start: 0.8257 (m) cc_final: 0.7910 (p) REVERT: E 223 ASP cc_start: 0.7920 (m-30) cc_final: 0.7483 (m-30) REVERT: R 165 MET cc_start: 0.8603 (ttm) cc_final: 0.7986 (tmm) REVERT: R 173 MET cc_start: 0.6932 (tmm) cc_final: 0.6301 (tpt) REVERT: R 250 TYR cc_start: 0.8172 (m-10) cc_final: 0.7343 (m-10) REVERT: R 279 LEU cc_start: 0.8005 (mp) cc_final: 0.7784 (mt) REVERT: R 304 MET cc_start: 0.7263 (ptm) cc_final: 0.7053 (ttm) REVERT: R 313 GLN cc_start: 0.7184 (tt0) cc_final: 0.6811 (mt0) REVERT: R 366 ILE cc_start: 0.7800 (mt) cc_final: 0.7597 (mp) REVERT: R 387 PHE cc_start: 0.7827 (t80) cc_final: 0.7607 (t80) outliers start: 24 outliers final: 13 residues processed: 160 average time/residue: 0.4858 time to fit residues: 82.3041 Evaluate side-chains 154 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 95 optimal weight: 0.1980 chunk 96 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 269 ASN B 268 ASN E 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.171248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119828 restraints weight = 10126.106| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.06 r_work: 0.3251 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9013 Z= 0.104 Angle : 0.466 8.105 12239 Z= 0.245 Chirality : 0.041 0.141 1406 Planarity : 0.003 0.048 1547 Dihedral : 3.858 31.721 1232 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.21 % Allowed : 14.29 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.25), residues: 1129 helix: 2.50 (0.26), residues: 405 sheet: 0.62 (0.29), residues: 288 loop : 0.45 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 160 TYR 0.014 0.001 TYR E 190 PHE 0.009 0.001 PHE B 199 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 9010) covalent geometry : angle 0.46545 (12233) SS BOND : bond 0.00284 ( 3) SS BOND : angle 0.67975 ( 6) hydrogen bonds : bond 0.03585 ( 459) hydrogen bonds : angle 4.44672 ( 1299) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.271 Fit side-chains REVERT: A 29 LYS cc_start: 0.8186 (tttt) cc_final: 0.7677 (ttmm) REVERT: A 186 GLU cc_start: 0.8330 (tt0) cc_final: 0.7679 (tt0) REVERT: A 197 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8020 (mtpp) REVERT: A 208 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7488 (ttp80) REVERT: A 209 LYS cc_start: 0.8379 (pttt) cc_final: 0.8065 (ptmt) REVERT: A 251 ASP cc_start: 0.8035 (t70) cc_final: 0.7702 (t0) REVERT: A 330 LYS cc_start: 0.7653 (mttt) cc_final: 0.7041 (mtpt) REVERT: B 19 ARG cc_start: 0.7014 (ttp80) cc_final: 0.6570 (ttp80) REVERT: B 46 ARG cc_start: 0.8024 (mtp-110) cc_final: 0.7280 (mmt-90) REVERT: B 129 ARG cc_start: 0.8313 (mtp180) cc_final: 0.7727 (mmt180) REVERT: B 226 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8106 (mp0) REVERT: C 21 MET cc_start: 0.8722 (mmm) cc_final: 0.7832 (ttt) REVERT: C 46 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7829 (pttp) REVERT: E 6 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: E 43 LYS cc_start: 0.8189 (mptm) cc_final: 0.7847 (mptt) REVERT: E 77 ASN cc_start: 0.8534 (m-40) cc_final: 0.8302 (m-40) REVERT: E 145 SER cc_start: 0.8205 (m) cc_final: 0.7857 (p) REVERT: E 160 ARG cc_start: 0.7068 (ttp-110) cc_final: 0.6750 (ttp-110) REVERT: E 223 ASP cc_start: 0.7772 (m-30) cc_final: 0.7491 (m-30) REVERT: R 165 MET cc_start: 0.8522 (ttm) cc_final: 0.7891 (tmm) REVERT: R 173 MET cc_start: 0.7164 (tmm) cc_final: 0.6113 (tpt) REVERT: R 250 TYR cc_start: 0.8177 (m-10) cc_final: 0.7352 (m-10) REVERT: R 304 MET cc_start: 0.6990 (ptm) cc_final: 0.6768 (ttm) REVERT: R 366 ILE cc_start: 0.7796 (mt) cc_final: 0.7564 (mp) REVERT: R 387 PHE cc_start: 0.7819 (t80) cc_final: 0.7569 (t80) outliers start: 21 outliers final: 6 residues processed: 161 average time/residue: 0.4582 time to fit residues: 78.1162 Evaluate side-chains 151 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 99 optimal weight: 30.0000 chunk 30 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.168720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.116265 restraints weight = 10154.890| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.06 r_work: 0.3196 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9013 Z= 0.169 Angle : 0.523 11.884 12239 Z= 0.272 Chirality : 0.043 0.145 1406 Planarity : 0.004 0.047 1547 Dihedral : 4.107 36.011 1232 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.21 % Allowed : 15.23 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.25), residues: 1129 helix: 2.42 (0.26), residues: 405 sheet: 0.51 (0.30), residues: 272 loop : 0.31 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.012 0.001 TYR R 380 PHE 0.014 0.001 PHE A 196 TRP 0.016 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9010) covalent geometry : angle 0.52253 (12233) SS BOND : bond 0.00252 ( 3) SS BOND : angle 1.04975 ( 6) hydrogen bonds : bond 0.03894 ( 459) hydrogen bonds : angle 4.58987 ( 1299) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.217 Fit side-chains REVERT: A 29 LYS cc_start: 0.8285 (tttt) cc_final: 0.7772 (ttmm) REVERT: A 186 GLU cc_start: 0.8399 (tt0) cc_final: 0.7645 (tt0) REVERT: A 197 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8032 (mtpp) REVERT: A 208 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7514 (ttp80) REVERT: A 209 LYS cc_start: 0.8440 (pttt) cc_final: 0.8117 (ptmt) REVERT: A 330 LYS cc_start: 0.7669 (mttt) cc_final: 0.7071 (mtpt) REVERT: B 19 ARG cc_start: 0.7039 (ttp80) cc_final: 0.6595 (ttp80) REVERT: B 46 ARG cc_start: 0.8083 (mtp-110) cc_final: 0.7319 (mmt-90) REVERT: B 129 ARG cc_start: 0.8313 (mtp180) cc_final: 0.7742 (mmt180) REVERT: B 226 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8102 (mp0) REVERT: C 21 MET cc_start: 0.8758 (mmm) cc_final: 0.7838 (ttt) REVERT: C 46 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7853 (pttp) REVERT: E 43 LYS cc_start: 0.8167 (mptm) cc_final: 0.7819 (mptt) REVERT: E 77 ASN cc_start: 0.8591 (m-40) cc_final: 0.8341 (m-40) REVERT: E 145 SER cc_start: 0.8230 (m) cc_final: 0.7891 (p) REVERT: E 223 ASP cc_start: 0.7954 (m-30) cc_final: 0.7704 (m-30) REVERT: E 230 MET cc_start: 0.9135 (ttp) cc_final: 0.8773 (ttp) REVERT: R 165 MET cc_start: 0.8492 (ttm) cc_final: 0.7820 (tmm) REVERT: R 173 MET cc_start: 0.6873 (tmm) cc_final: 0.6313 (tpt) REVERT: R 250 TYR cc_start: 0.8192 (m-10) cc_final: 0.7383 (m-10) REVERT: R 299 ARG cc_start: 0.7525 (mtp85) cc_final: 0.7101 (mmm-85) REVERT: R 303 ARG cc_start: 0.7247 (mmm160) cc_final: 0.6891 (mmm-85) REVERT: R 304 MET cc_start: 0.7385 (ptm) cc_final: 0.6999 (ttm) REVERT: R 366 ILE cc_start: 0.7758 (mt) cc_final: 0.7528 (mp) outliers start: 21 outliers final: 12 residues processed: 154 average time/residue: 0.5449 time to fit residues: 88.4276 Evaluate side-chains 157 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 206 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 77 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 269 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.169100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116918 restraints weight = 10163.463| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.05 r_work: 0.3203 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9013 Z= 0.153 Angle : 0.504 7.761 12239 Z= 0.265 Chirality : 0.043 0.143 1406 Planarity : 0.004 0.050 1547 Dihedral : 4.140 38.642 1232 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.31 % Allowed : 15.34 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.25), residues: 1129 helix: 2.45 (0.26), residues: 405 sheet: 0.49 (0.30), residues: 277 loop : 0.31 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 160 TYR 0.015 0.001 TYR R 280 PHE 0.013 0.001 PHE A 196 TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9010) covalent geometry : angle 0.50367 (12233) SS BOND : bond 0.00271 ( 3) SS BOND : angle 0.84702 ( 6) hydrogen bonds : bond 0.03768 ( 459) hydrogen bonds : angle 4.56406 ( 1299) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.240 Fit side-chains REVERT: A 29 LYS cc_start: 0.8282 (tttt) cc_final: 0.7769 (ttmm) REVERT: A 186 GLU cc_start: 0.8380 (tt0) cc_final: 0.7655 (tt0) REVERT: A 197 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.7940 (mtpp) REVERT: A 208 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7522 (ttp80) REVERT: A 209 LYS cc_start: 0.8403 (pttt) cc_final: 0.8106 (ptmt) REVERT: A 255 ASN cc_start: 0.8492 (m-40) cc_final: 0.8210 (m110) REVERT: A 330 LYS cc_start: 0.7682 (mttt) cc_final: 0.7083 (mtpt) REVERT: B 19 ARG cc_start: 0.7052 (ttp80) cc_final: 0.6617 (ttp80) REVERT: B 46 ARG cc_start: 0.8129 (mtp-110) cc_final: 0.7314 (mmt-90) REVERT: B 129 ARG cc_start: 0.8247 (mtp180) cc_final: 0.7763 (mmt180) REVERT: B 226 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8117 (mp0) REVERT: C 21 MET cc_start: 0.8780 (mmm) cc_final: 0.7865 (ttt) REVERT: C 46 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7840 (pttp) REVERT: E 43 LYS cc_start: 0.8262 (mptm) cc_final: 0.7902 (mptt) REVERT: E 77 ASN cc_start: 0.8582 (m-40) cc_final: 0.8326 (m-40) REVERT: E 145 SER cc_start: 0.8228 (m) cc_final: 0.7896 (p) REVERT: E 160 ARG cc_start: 0.7053 (ttp-110) cc_final: 0.6709 (ttp-110) REVERT: E 230 MET cc_start: 0.9133 (ttp) cc_final: 0.8781 (ttp) REVERT: R 165 MET cc_start: 0.8445 (ttm) cc_final: 0.8037 (tmm) REVERT: R 173 MET cc_start: 0.6999 (tmm) cc_final: 0.6239 (tpt) REVERT: R 250 TYR cc_start: 0.8195 (m-10) cc_final: 0.7325 (m-10) REVERT: R 299 ARG cc_start: 0.7590 (mtp85) cc_final: 0.7161 (mmm-85) REVERT: R 303 ARG cc_start: 0.7246 (mmm160) cc_final: 0.6794 (mmm-85) outliers start: 22 outliers final: 12 residues processed: 155 average time/residue: 0.5729 time to fit residues: 93.3798 Evaluate side-chains 156 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 206 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 72 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** A 204 GLN A 269 ASN B 32 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.170842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.119225 restraints weight = 10122.471| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.04 r_work: 0.3246 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9013 Z= 0.106 Angle : 0.486 12.362 12239 Z= 0.251 Chirality : 0.041 0.156 1406 Planarity : 0.003 0.048 1547 Dihedral : 3.966 36.504 1232 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.89 % Allowed : 16.60 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.25), residues: 1129 helix: 2.57 (0.26), residues: 405 sheet: 0.53 (0.30), residues: 272 loop : 0.33 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 160 TYR 0.013 0.001 TYR E 190 PHE 0.009 0.001 PHE B 199 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9010) covalent geometry : angle 0.48616 (12233) SS BOND : bond 0.00299 ( 3) SS BOND : angle 0.65744 ( 6) hydrogen bonds : bond 0.03411 ( 459) hydrogen bonds : angle 4.39627 ( 1299) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.208 Fit side-chains REVERT: A 29 LYS cc_start: 0.8113 (tttt) cc_final: 0.7603 (ttmm) REVERT: A 186 GLU cc_start: 0.8393 (tt0) cc_final: 0.7930 (tt0) REVERT: A 208 ARG cc_start: 0.7886 (ttm-80) cc_final: 0.7430 (ttp80) REVERT: A 209 LYS cc_start: 0.8340 (pttt) cc_final: 0.8033 (ptmt) REVERT: A 255 ASN cc_start: 0.8357 (m-40) cc_final: 0.8061 (m110) REVERT: A 306 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7433 (mm-40) REVERT: A 310 LEU cc_start: 0.8873 (mt) cc_final: 0.8481 (mt) REVERT: A 330 LYS cc_start: 0.7572 (mttt) cc_final: 0.6963 (mtpt) REVERT: B 19 ARG cc_start: 0.6978 (ttp80) cc_final: 0.6547 (ttp80) REVERT: B 46 ARG cc_start: 0.8030 (mtp-110) cc_final: 0.7225 (mmt-90) REVERT: B 129 ARG cc_start: 0.8234 (mtp180) cc_final: 0.7716 (mmt180) REVERT: B 226 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8080 (mp0) REVERT: C 21 MET cc_start: 0.8752 (mmm) cc_final: 0.7830 (ttt) REVERT: C 46 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7801 (pttp) REVERT: E 6 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7404 (mt-10) REVERT: E 43 LYS cc_start: 0.8234 (mptm) cc_final: 0.7871 (mptt) REVERT: E 77 ASN cc_start: 0.8507 (m-40) cc_final: 0.8280 (m-40) REVERT: E 82 GLN cc_start: 0.8382 (tp40) cc_final: 0.8156 (tp-100) REVERT: E 145 SER cc_start: 0.8148 (m) cc_final: 0.7854 (p) REVERT: E 160 ARG cc_start: 0.6954 (ttp-110) cc_final: 0.6625 (ttp-110) REVERT: E 230 MET cc_start: 0.9118 (ttp) cc_final: 0.8761 (ttp) REVERT: R 165 MET cc_start: 0.8421 (ttm) cc_final: 0.7746 (tmm) REVERT: R 173 MET cc_start: 0.6876 (tmm) cc_final: 0.6311 (tpt) REVERT: R 250 TYR cc_start: 0.8149 (m-10) cc_final: 0.7358 (m-10) REVERT: R 299 ARG cc_start: 0.7473 (mtp85) cc_final: 0.7028 (mmm-85) REVERT: R 303 ARG cc_start: 0.7173 (mmm160) cc_final: 0.6735 (mmm-85) outliers start: 18 outliers final: 13 residues processed: 157 average time/residue: 0.5645 time to fit residues: 93.2311 Evaluate side-chains 158 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 23 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 204 GLN B 32 GLN B 268 ASN E 183 GLN R 179 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.168275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115722 restraints weight = 10057.885| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.05 r_work: 0.3202 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9013 Z= 0.194 Angle : 0.531 8.695 12239 Z= 0.279 Chirality : 0.044 0.158 1406 Planarity : 0.004 0.048 1547 Dihedral : 4.249 41.708 1232 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.21 % Allowed : 16.28 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.25), residues: 1129 helix: 2.40 (0.26), residues: 405 sheet: 0.44 (0.30), residues: 277 loop : 0.30 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 160 TYR 0.015 0.002 TYR R 380 PHE 0.015 0.002 PHE A 196 TRP 0.017 0.002 TRP B 339 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9010) covalent geometry : angle 0.53083 (12233) SS BOND : bond 0.00256 ( 3) SS BOND : angle 1.08969 ( 6) hydrogen bonds : bond 0.03906 ( 459) hydrogen bonds : angle 4.63567 ( 1299) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.199 Fit side-chains REVERT: A 29 LYS cc_start: 0.8271 (tttt) cc_final: 0.7754 (ttmm) REVERT: A 186 GLU cc_start: 0.8459 (tt0) cc_final: 0.7870 (tt0) REVERT: A 208 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7518 (ttp80) REVERT: A 209 LYS cc_start: 0.8404 (pttt) cc_final: 0.8094 (ptmt) REVERT: A 255 ASN cc_start: 0.8461 (m-40) cc_final: 0.8199 (m110) REVERT: A 330 LYS cc_start: 0.7716 (mttt) cc_final: 0.7076 (mtpt) REVERT: B 19 ARG cc_start: 0.7023 (ttp80) cc_final: 0.6642 (ttm110) REVERT: B 46 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7361 (mmt-90) REVERT: B 129 ARG cc_start: 0.8162 (mtp180) cc_final: 0.7631 (mmt180) REVERT: B 226 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8059 (mp0) REVERT: C 21 MET cc_start: 0.8778 (mmm) cc_final: 0.7909 (ttt) REVERT: C 46 LYS cc_start: 0.8217 (mmtt) cc_final: 0.8000 (pttp) REVERT: E 43 LYS cc_start: 0.8248 (mptm) cc_final: 0.7894 (mptt) REVERT: E 77 ASN cc_start: 0.8592 (m-40) cc_final: 0.8355 (m-40) REVERT: E 145 SER cc_start: 0.8194 (m) cc_final: 0.7853 (p) REVERT: E 160 ARG cc_start: 0.7063 (ttp-110) cc_final: 0.6745 (ttp-110) REVERT: E 180 ARG cc_start: 0.8590 (mtt-85) cc_final: 0.8133 (mtt-85) REVERT: E 230 MET cc_start: 0.9148 (ttp) cc_final: 0.8801 (ttp) REVERT: R 165 MET cc_start: 0.8481 (ttm) cc_final: 0.7807 (tmm) REVERT: R 173 MET cc_start: 0.6980 (tmm) cc_final: 0.6303 (tpt) REVERT: R 250 TYR cc_start: 0.8180 (m-10) cc_final: 0.7387 (m-10) REVERT: R 299 ARG cc_start: 0.7565 (mtp85) cc_final: 0.7045 (mmm-85) REVERT: R 303 ARG cc_start: 0.7293 (mmm160) cc_final: 0.6866 (mmm-85) outliers start: 21 outliers final: 15 residues processed: 151 average time/residue: 0.5823 time to fit residues: 92.3480 Evaluate side-chains 156 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.0980 chunk 82 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 269 ASN A 346 ASN B 32 GLN B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.170446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.118647 restraints weight = 10081.853| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.05 r_work: 0.3229 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9013 Z= 0.110 Angle : 0.490 12.632 12239 Z= 0.254 Chirality : 0.042 0.155 1406 Planarity : 0.003 0.048 1547 Dihedral : 4.048 40.025 1232 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.68 % Allowed : 17.02 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.25), residues: 1129 helix: 2.55 (0.26), residues: 403 sheet: 0.46 (0.30), residues: 272 loop : 0.24 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 160 TYR 0.013 0.001 TYR E 190 PHE 0.010 0.001 PHE B 199 TRP 0.012 0.001 TRP B 339 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9010) covalent geometry : angle 0.48969 (12233) SS BOND : bond 0.00276 ( 3) SS BOND : angle 0.74510 ( 6) hydrogen bonds : bond 0.03421 ( 459) hydrogen bonds : angle 4.44493 ( 1299) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.212 Fit side-chains REVERT: A 29 LYS cc_start: 0.8144 (tttt) cc_final: 0.7643 (ttmm) REVERT: A 186 GLU cc_start: 0.8412 (tt0) cc_final: 0.7938 (tt0) REVERT: A 208 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7450 (ttp80) REVERT: A 209 LYS cc_start: 0.8354 (pttt) cc_final: 0.8044 (ptmt) REVERT: A 255 ASN cc_start: 0.8366 (m-40) cc_final: 0.8064 (m110) REVERT: A 306 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7491 (mm-40) REVERT: A 330 LYS cc_start: 0.7621 (mttt) cc_final: 0.6981 (mtpt) REVERT: B 19 ARG cc_start: 0.6986 (ttp80) cc_final: 0.6612 (ttp80) REVERT: B 46 ARG cc_start: 0.8150 (mtp-110) cc_final: 0.7329 (mmt-90) REVERT: B 129 ARG cc_start: 0.8204 (mtp180) cc_final: 0.7638 (mmt180) REVERT: B 134 ARG cc_start: 0.8531 (ptm-80) cc_final: 0.8243 (ptt-90) REVERT: B 226 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8060 (mp0) REVERT: C 21 MET cc_start: 0.8760 (mmm) cc_final: 0.7872 (ttt) REVERT: C 46 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7871 (pttp) REVERT: E 6 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: E 43 LYS cc_start: 0.8234 (mptm) cc_final: 0.7888 (mptt) REVERT: E 77 ASN cc_start: 0.8509 (m-40) cc_final: 0.8303 (m-40) REVERT: E 82 GLN cc_start: 0.8420 (tp40) cc_final: 0.8192 (tp-100) REVERT: E 145 SER cc_start: 0.8218 (m) cc_final: 0.7878 (p) REVERT: E 160 ARG cc_start: 0.6995 (ttp-110) cc_final: 0.6675 (ttp-110) REVERT: E 180 ARG cc_start: 0.8568 (mtt-85) cc_final: 0.8154 (mtt-85) REVERT: E 230 MET cc_start: 0.9116 (ttp) cc_final: 0.8768 (ttp) REVERT: R 165 MET cc_start: 0.8395 (ttm) cc_final: 0.7687 (tmm) REVERT: R 173 MET cc_start: 0.6880 (tmm) cc_final: 0.6510 (tpt) REVERT: R 250 TYR cc_start: 0.8091 (m-10) cc_final: 0.7290 (m-10) REVERT: R 299 ARG cc_start: 0.7505 (mtp85) cc_final: 0.7067 (mmm-85) REVERT: R 303 ARG cc_start: 0.7208 (mmm160) cc_final: 0.6708 (mmm-85) outliers start: 16 outliers final: 10 residues processed: 149 average time/residue: 0.6105 time to fit residues: 95.4953 Evaluate side-chains 153 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 204 GLN A 269 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.170006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117876 restraints weight = 10031.634| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.04 r_work: 0.3231 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9013 Z= 0.128 Angle : 0.493 8.555 12239 Z= 0.257 Chirality : 0.042 0.142 1406 Planarity : 0.003 0.047 1547 Dihedral : 4.058 39.651 1232 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.79 % Allowed : 16.91 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.25), residues: 1129 helix: 2.55 (0.26), residues: 403 sheet: 0.40 (0.30), residues: 277 loop : 0.27 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 160 TYR 0.012 0.001 TYR R 380 PHE 0.011 0.001 PHE A 196 TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9010) covalent geometry : angle 0.49311 (12233) SS BOND : bond 0.00261 ( 3) SS BOND : angle 0.84432 ( 6) hydrogen bonds : bond 0.03508 ( 459) hydrogen bonds : angle 4.43937 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2924.28 seconds wall clock time: 50 minutes 38.87 seconds (3038.87 seconds total)