Starting phenix.real_space_refine on Sat Jun 7 11:24:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwh_37888/06_2025/8wwh_37888.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwh_37888/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wwh_37888/06_2025/8wwh_37888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwh_37888/06_2025/8wwh_37888.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwh_37888/06_2025/8wwh_37888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwh_37888/06_2025/8wwh_37888.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.072 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 5.38, per 1000 atoms: 0.61 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: 2.29 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.08 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: 2.81 Time building geometry restraints manager: 2.72 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.330 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.310 ------------------------------------------------------------------------------- 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 : 4.75 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 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 TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS B 183 PHE 0.010 0.001 PHE A 196 TYR 0.009 0.001 TYR R 280 ARG 0.002 0.000 ARG R 325 Details of bonding type rmsd hydrogen bonds : bond 0.23411 ( 459) hydrogen bonds : angle 7.39105 ( 1299) SS BOND : bond 0.00086 ( 3) SS BOND : angle 0.73772 ( 6) covalent geometry : bond 0.00303 ( 9010) covalent geometry : angle 0.42072 (12233) *********************** 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 : 0.998 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: 1.2982 time to fit residues: 260.2093 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 : 0.969 ------------------------------------------------------------------------------- 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 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.170230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.117712 restraints weight = 9964.855| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.98 r_work: 0.3173 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9013 Z= 0.132 Angle : 0.510 9.508 12239 Z= 0.276 Chirality : 0.042 0.153 1406 Planarity : 0.004 0.058 1547 Dihedral : 4.324 56.090 1236 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.73 % Allowed : 9.24 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.25), residues: 1129 helix: 2.06 (0.26), residues: 403 sheet: 0.86 (0.30), residues: 278 loop : 0.33 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.018 0.001 PHE R 116 TYR 0.015 0.001 TYR E 190 ARG 0.007 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.05096 ( 459) hydrogen bonds : angle 4.96769 ( 1299) SS BOND : bond 0.00291 ( 3) SS BOND : angle 0.84193 ( 6) covalent geometry : bond 0.00272 ( 9010) covalent geometry : angle 0.50969 (12233) *********************** 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 : 1.079 Fit side-chains REVERT: A 29 LYS cc_start: 0.8529 (tttt) cc_final: 0.8071 (ttmm) REVERT: A 186 GLU cc_start: 0.8372 (tt0) cc_final: 0.7939 (tt0) REVERT: A 208 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7665 (ttp80) REVERT: A 209 LYS cc_start: 0.8547 (pttt) cc_final: 0.8255 (ptmt) REVERT: A 309 ASP cc_start: 0.7968 (t70) cc_final: 0.7677 (t0) REVERT: A 330 LYS cc_start: 0.7703 (mttt) cc_final: 0.7097 (mtpt) REVERT: B 19 ARG cc_start: 0.6943 (ttp80) cc_final: 0.6512 (ttm110) REVERT: B 46 ARG cc_start: 0.8138 (mtp-110) cc_final: 0.7462 (mmt-90) REVERT: B 129 ARG cc_start: 0.8319 (mtp180) cc_final: 0.7753 (mmt180) REVERT: B 226 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8178 (mp0) REVERT: C 21 MET cc_start: 0.8694 (mmm) cc_final: 0.7929 (ttt) REVERT: C 46 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7991 (pttp) REVERT: E 43 LYS cc_start: 0.8536 (mmtm) cc_final: 0.8241 (mptp) REVERT: E 77 ASN cc_start: 0.8523 (m-40) cc_final: 0.8271 (m-40) REVERT: E 223 ASP cc_start: 0.7733 (m-30) cc_final: 0.7515 (m-30) REVERT: R 165 MET cc_start: 0.8615 (ttm) cc_final: 0.7986 (tmm) REVERT: R 173 MET cc_start: 0.7000 (tmm) cc_final: 0.6377 (tpt) REVERT: R 274 LEU cc_start: 0.7212 (tp) cc_final: 0.7010 (tp) REVERT: R 313 GLN cc_start: 0.7302 (tt0) cc_final: 0.6905 (mt0) outliers start: 26 outliers final: 12 residues processed: 166 average time/residue: 1.4004 time to fit residues: 246.9049 Evaluate side-chains 147 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 253 ILE 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 10 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 79 optimal weight: 0.2980 chunk 62 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.165716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.121434 restraints weight = 10056.533| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.35 r_work: 0.3100 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 9013 Z= 0.286 Angle : 0.605 8.875 12239 Z= 0.323 Chirality : 0.047 0.160 1406 Planarity : 0.005 0.055 1547 Dihedral : 4.508 40.089 1232 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.05 % Allowed : 12.39 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.25), residues: 1129 helix: 1.99 (0.26), residues: 403 sheet: 0.54 (0.30), residues: 288 loop : 0.27 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.006 0.002 HIS B 142 PHE 0.017 0.002 PHE A 196 TYR 0.018 0.002 TYR R 280 ARG 0.009 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 459) hydrogen bonds : angle 5.08731 ( 1299) SS BOND : bond 0.00288 ( 3) SS BOND : angle 1.63569 ( 6) covalent geometry : bond 0.00670 ( 9010) covalent geometry : angle 0.60358 (12233) *********************** 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 183 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.898 Fit side-chains REVERT: A 29 LYS cc_start: 0.8820 (tttt) cc_final: 0.8391 (ttmm) REVERT: A 53 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7714 (mtp) REVERT: A 186 GLU cc_start: 0.8488 (tt0) cc_final: 0.8023 (tt0) REVERT: A 207 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: A 208 ARG cc_start: 0.8084 (ttm-80) cc_final: 0.7790 (ttp80) REVERT: A 209 LYS cc_start: 0.8602 (pttt) cc_final: 0.8277 (ptmt) REVERT: A 309 ASP cc_start: 0.8070 (t70) cc_final: 0.7798 (t0) REVERT: A 330 LYS cc_start: 0.7836 (mttt) cc_final: 0.7238 (mtpt) REVERT: B 17 GLN cc_start: 0.7613 (tm-30) cc_final: 0.7377 (tm-30) REVERT: B 19 ARG cc_start: 0.7099 (ttp80) cc_final: 0.6694 (ttm110) REVERT: B 46 ARG cc_start: 0.8231 (mtp-110) cc_final: 0.7592 (mmt-90) REVERT: B 129 ARG cc_start: 0.8293 (mtp180) cc_final: 0.7852 (mmt180) REVERT: B 226 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8177 (mp0) REVERT: B 262 MET cc_start: 0.8820 (tpp) cc_final: 0.8494 (tpp) REVERT: C 21 MET cc_start: 0.8748 (mmm) cc_final: 0.7857 (ttt) REVERT: C 46 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7999 (pttp) REVERT: E 43 LYS cc_start: 0.8704 (mmtm) cc_final: 0.8427 (mptp) REVERT: E 93 MET cc_start: 0.8629 (tpp) cc_final: 0.8413 (tpp) REVERT: E 145 SER cc_start: 0.8406 (m) cc_final: 0.8050 (p) REVERT: E 160 ARG cc_start: 0.7320 (ttp-110) cc_final: 0.7068 (ttp-110) REVERT: E 223 ASP cc_start: 0.8140 (m-30) cc_final: 0.7794 (m-30) REVERT: E 230 MET cc_start: 0.9181 (ttp) cc_final: 0.8830 (ttp) REVERT: R 173 MET cc_start: 0.7233 (tmm) cc_final: 0.6032 (tpt) REVERT: R 279 LEU cc_start: 0.8017 (mt) cc_final: 0.7812 (mp) REVERT: R 283 PHE cc_start: 0.7427 (t80) cc_final: 0.7224 (m-10) REVERT: R 303 ARG cc_start: 0.7020 (mmm160) cc_final: 0.6784 (mmm-85) REVERT: R 313 GLN cc_start: 0.7528 (tt0) cc_final: 0.7063 (mt0) REVERT: R 366 ILE cc_start: 0.7971 (mt) cc_final: 0.7741 (mp) REVERT: R 387 PHE cc_start: 0.7897 (t80) cc_final: 0.7678 (t80) outliers start: 29 outliers final: 15 residues processed: 164 average time/residue: 1.2956 time to fit residues: 225.1871 Evaluate side-chains 160 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 207 GLU 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 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 184 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 347 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 0.0980 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 98 optimal weight: 0.0370 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 255 ASN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.169849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.117730 restraints weight = 9968.487| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.98 r_work: 0.3188 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9013 Z= 0.109 Angle : 0.487 10.597 12239 Z= 0.257 Chirality : 0.042 0.150 1406 Planarity : 0.004 0.056 1547 Dihedral : 4.077 37.495 1232 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.10 % Allowed : 13.87 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.25), residues: 1129 helix: 2.35 (0.26), residues: 403 sheet: 0.61 (0.30), residues: 281 loop : 0.36 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.010 0.001 PHE B 199 TYR 0.017 0.001 TYR R 280 ARG 0.006 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 459) hydrogen bonds : angle 4.62662 ( 1299) SS BOND : bond 0.00359 ( 3) SS BOND : angle 0.68883 ( 6) covalent geometry : bond 0.00228 ( 9010) covalent geometry : angle 0.48697 (12233) *********************** 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 179 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8454 (tttt) cc_final: 0.7951 (ttmm) REVERT: A 186 GLU cc_start: 0.8375 (tt0) cc_final: 0.7719 (tt0) REVERT: A 197 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8238 (mtpp) REVERT: A 208 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7661 (ttp80) REVERT: A 209 LYS cc_start: 0.8516 (pttt) cc_final: 0.8206 (ptmt) REVERT: A 330 LYS cc_start: 0.7784 (mttt) cc_final: 0.7188 (mtpt) REVERT: B 17 GLN cc_start: 0.7595 (tm-30) cc_final: 0.7287 (tm-30) REVERT: B 19 ARG cc_start: 0.7074 (ttp80) cc_final: 0.6639 (ttp80) REVERT: B 46 ARG cc_start: 0.8090 (mtp-110) cc_final: 0.7464 (mmt-90) REVERT: B 129 ARG cc_start: 0.8311 (mtp180) cc_final: 0.7818 (mmt180) REVERT: B 226 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8191 (mp0) REVERT: C 21 MET cc_start: 0.8738 (mmm) cc_final: 0.7847 (ttt) REVERT: C 46 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7969 (pttp) REVERT: E 43 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8432 (mptm) REVERT: E 145 SER cc_start: 0.8267 (m) cc_final: 0.7953 (p) REVERT: E 223 ASP cc_start: 0.7996 (m-30) cc_final: 0.7548 (m-30) REVERT: R 173 MET cc_start: 0.6902 (tmm) cc_final: 0.6292 (tpt) REVERT: R 250 TYR cc_start: 0.8146 (m-10) cc_final: 0.7363 (m-10) REVERT: R 313 GLN cc_start: 0.7256 (tt0) cc_final: 0.6898 (mt0) REVERT: R 366 ILE cc_start: 0.7857 (mt) cc_final: 0.7647 (mp) outliers start: 20 outliers final: 8 residues processed: 167 average time/residue: 1.3042 time to fit residues: 231.0686 Evaluate side-chains 151 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 38 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 155 VAL 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 18 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.170338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118239 restraints weight = 10036.668| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.05 r_work: 0.3236 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2421 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= 0.115 Angle : 0.483 7.993 12239 Z= 0.254 Chirality : 0.042 0.144 1406 Planarity : 0.004 0.048 1547 Dihedral : 3.970 35.983 1232 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.31 % Allowed : 14.92 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.25), residues: 1129 helix: 2.44 (0.26), residues: 403 sheet: 0.60 (0.30), residues: 275 loop : 0.34 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS A 188 PHE 0.011 0.001 PHE A 196 TYR 0.015 0.001 TYR R 280 ARG 0.012 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 459) hydrogen bonds : angle 4.51920 ( 1299) SS BOND : bond 0.00282 ( 3) SS BOND : angle 0.77063 ( 6) covalent geometry : bond 0.00252 ( 9010) covalent geometry : angle 0.48329 (12233) *********************** 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 176 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.875 Fit side-chains REVERT: A 29 LYS cc_start: 0.8197 (tttt) cc_final: 0.7667 (ttmm) REVERT: A 186 GLU cc_start: 0.8365 (tt0) cc_final: 0.7611 (tt0) REVERT: A 197 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8065 (mtpp) REVERT: A 208 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7453 (ttp80) REVERT: A 209 LYS cc_start: 0.8379 (pttt) cc_final: 0.8055 (ptmt) REVERT: A 330 LYS cc_start: 0.7656 (mttt) cc_final: 0.7024 (mtpt) REVERT: B 19 ARG cc_start: 0.7002 (ttp80) cc_final: 0.6559 (ttp80) REVERT: B 46 ARG cc_start: 0.7986 (mtp-110) cc_final: 0.7265 (mmt-90) REVERT: B 129 ARG cc_start: 0.8302 (mtp180) cc_final: 0.7723 (mmt180) REVERT: B 226 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8101 (mp0) REVERT: C 21 MET cc_start: 0.8730 (mmm) cc_final: 0.7822 (ttt) REVERT: C 46 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7986 (pttp) REVERT: E 43 LYS cc_start: 0.8490 (mmtm) cc_final: 0.8253 (mptm) REVERT: E 145 SER cc_start: 0.8211 (m) cc_final: 0.7873 (p) REVERT: E 160 ARG cc_start: 0.7056 (ttp-110) cc_final: 0.6732 (ttp-110) REVERT: E 223 ASP cc_start: 0.7777 (m-30) cc_final: 0.7512 (m-30) REVERT: E 230 MET cc_start: 0.9116 (ttp) cc_final: 0.8767 (ttp) REVERT: R 173 MET cc_start: 0.7168 (tmm) cc_final: 0.6261 (tpt) REVERT: R 250 TYR cc_start: 0.8157 (m-10) cc_final: 0.7316 (m-10) REVERT: R 313 GLN cc_start: 0.7120 (tt0) cc_final: 0.6771 (mt0) REVERT: R 366 ILE cc_start: 0.7769 (mt) cc_final: 0.7552 (mp) REVERT: R 387 PHE cc_start: 0.7758 (t80) cc_final: 0.7537 (t80) outliers start: 22 outliers final: 10 residues processed: 164 average time/residue: 1.2859 time to fit residues: 224.2962 Evaluate side-chains 158 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 B residue 331 SER Chi-restraints excluded: chain E residue 23 SER 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 3 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 255 ASN A 269 ASN B 268 ASN R 179 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.166703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.114032 restraints weight = 9996.954| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.96 r_work: 0.3145 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9013 Z= 0.207 Angle : 0.554 11.946 12239 Z= 0.287 Chirality : 0.044 0.150 1406 Planarity : 0.004 0.048 1547 Dihedral : 4.309 41.530 1232 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.73 % Allowed : 15.13 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1129 helix: 2.30 (0.26), residues: 403 sheet: 0.46 (0.30), residues: 270 loop : 0.21 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.004 0.001 HIS B 183 PHE 0.016 0.002 PHE A 196 TYR 0.012 0.002 TYR R 280 ARG 0.007 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 459) hydrogen bonds : angle 4.75238 ( 1299) SS BOND : bond 0.00259 ( 3) SS BOND : angle 1.12955 ( 6) covalent geometry : bond 0.00479 ( 9010) covalent geometry : angle 0.55325 (12233) *********************** 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 179 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.013 Fit side-chains REVERT: A 29 LYS cc_start: 0.8454 (tttt) cc_final: 0.7956 (ttmm) REVERT: A 186 GLU cc_start: 0.8433 (tt0) cc_final: 0.7811 (tt0) REVERT: A 197 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8202 (mtpp) REVERT: A 208 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7687 (ttp80) REVERT: A 209 LYS cc_start: 0.8523 (pttt) cc_final: 0.8224 (ptmt) REVERT: A 330 LYS cc_start: 0.7825 (mttt) cc_final: 0.7217 (mtpt) REVERT: B 19 ARG cc_start: 0.7084 (ttp80) cc_final: 0.6689 (ttm110) REVERT: B 33 ILE cc_start: 0.7850 (mm) cc_final: 0.7647 (mt) REVERT: B 46 ARG cc_start: 0.8124 (mtp-110) cc_final: 0.7510 (mmt-90) REVERT: B 129 ARG cc_start: 0.8261 (mtp180) cc_final: 0.7742 (mmt180) REVERT: B 226 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8124 (mp0) REVERT: C 21 MET cc_start: 0.8762 (mmm) cc_final: 0.7888 (ttt) REVERT: E 43 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8441 (mptm) REVERT: E 145 SER cc_start: 0.8250 (m) cc_final: 0.7924 (p) REVERT: E 223 ASP cc_start: 0.7978 (m-30) cc_final: 0.7662 (m-30) REVERT: E 230 MET cc_start: 0.9178 (ttp) cc_final: 0.8820 (ttp) REVERT: R 173 MET cc_start: 0.6940 (tmm) cc_final: 0.6380 (tpt) REVERT: R 250 TYR cc_start: 0.8224 (m-10) cc_final: 0.7474 (m-10) REVERT: R 313 GLN cc_start: 0.7360 (tt0) cc_final: 0.6917 (mt0) REVERT: R 380 TYR cc_start: 0.7464 (t80) cc_final: 0.7161 (t80) outliers start: 26 outliers final: 14 residues processed: 163 average time/residue: 1.4243 time to fit residues: 245.1310 Evaluate side-chains 164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 176 GLN 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 155 VAL Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 184 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 255 ASN 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 = 0.3868 r_free = 0.3868 target = 0.167104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122867 restraints weight = 10055.204| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.28 r_work: 0.3129 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9013 Z= 0.187 Angle : 0.536 7.858 12239 Z= 0.281 Chirality : 0.043 0.148 1406 Planarity : 0.004 0.051 1547 Dihedral : 4.328 44.667 1232 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.73 % Allowed : 15.65 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1129 helix: 2.30 (0.26), residues: 403 sheet: 0.36 (0.30), residues: 279 loop : 0.19 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.001 PHE A 196 TYR 0.015 0.002 TYR R 280 ARG 0.012 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 459) hydrogen bonds : angle 4.72213 ( 1299) SS BOND : bond 0.00297 ( 3) SS BOND : angle 1.02988 ( 6) covalent geometry : bond 0.00431 ( 9010) covalent geometry : angle 0.53568 (12233) *********************** 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 180 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.059 Fit side-chains REVERT: A 29 LYS cc_start: 0.8513 (tttt) cc_final: 0.8033 (ttmm) REVERT: A 186 GLU cc_start: 0.8410 (tt0) cc_final: 0.7785 (tt0) REVERT: A 197 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8291 (mtpp) REVERT: A 208 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7750 (ttp80) REVERT: A 209 LYS cc_start: 0.8518 (pttt) cc_final: 0.8252 (ptmt) REVERT: A 330 LYS cc_start: 0.7876 (mttt) cc_final: 0.7275 (mtpt) REVERT: B 19 ARG cc_start: 0.7115 (ttp80) cc_final: 0.6676 (ttp80) REVERT: B 46 ARG cc_start: 0.8207 (mtp-110) cc_final: 0.7580 (mmt-90) REVERT: B 129 ARG cc_start: 0.8256 (mtp180) cc_final: 0.7789 (mmt180) REVERT: B 226 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8194 (mp0) REVERT: C 21 MET cc_start: 0.8798 (mmm) cc_final: 0.7955 (ttt) REVERT: E 43 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8464 (mptm) REVERT: E 145 SER cc_start: 0.8253 (m) cc_final: 0.7942 (p) REVERT: E 160 ARG cc_start: 0.7281 (ttp-110) cc_final: 0.6944 (ttp-110) REVERT: E 223 ASP cc_start: 0.8032 (m-30) cc_final: 0.7802 (m-30) REVERT: E 230 MET cc_start: 0.9174 (ttp) cc_final: 0.8824 (ttp) REVERT: R 173 MET cc_start: 0.7099 (tmm) cc_final: 0.6382 (tpt) REVERT: R 250 TYR cc_start: 0.8295 (m-10) cc_final: 0.7511 (m-10) REVERT: R 313 GLN cc_start: 0.7441 (tt0) cc_final: 0.6958 (mt0) REVERT: R 345 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6823 (mp10) REVERT: R 380 TYR cc_start: 0.7475 (t80) cc_final: 0.7196 (t80) outliers start: 26 outliers final: 18 residues processed: 166 average time/residue: 1.4951 time to fit residues: 263.4339 Evaluate side-chains 168 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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 B residue 331 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 144 THR 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 Chi-restraints excluded: chain R residue 345 GLN 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 75 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 204 GLN A 269 ASN A 346 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 = 0.3899 r_free = 0.3899 target = 0.168972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.116575 restraints weight = 10203.319| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.05 r_work: 0.3212 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9013 Z= 0.146 Angle : 0.521 11.773 12239 Z= 0.269 Chirality : 0.043 0.146 1406 Planarity : 0.004 0.049 1547 Dihedral : 4.237 44.188 1232 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.52 % Allowed : 16.07 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1129 helix: 2.38 (0.26), residues: 403 sheet: 0.36 (0.30), residues: 279 loop : 0.21 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 PHE 0.014 0.001 PHE R 161 TYR 0.013 0.001 TYR R 280 ARG 0.011 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 459) hydrogen bonds : angle 4.63241 ( 1299) SS BOND : bond 0.00285 ( 3) SS BOND : angle 0.85342 ( 6) covalent geometry : bond 0.00331 ( 9010) covalent geometry : angle 0.52042 (12233) *********************** 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 177 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.883 Fit side-chains REVERT: A 29 LYS cc_start: 0.8262 (tttt) cc_final: 0.7733 (ttmm) REVERT: A 186 GLU cc_start: 0.8369 (tt0) cc_final: 0.7651 (tt0) REVERT: A 197 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8089 (mtpp) REVERT: A 208 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7535 (ttp80) REVERT: A 209 LYS cc_start: 0.8394 (pttt) cc_final: 0.8082 (ptmt) REVERT: A 330 LYS cc_start: 0.7669 (mttt) cc_final: 0.7012 (mtpt) REVERT: B 19 ARG cc_start: 0.7000 (ttp80) cc_final: 0.6622 (ttp80) REVERT: B 46 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7305 (mmt-90) REVERT: B 129 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7623 (mmt180) REVERT: B 226 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8096 (mp0) REVERT: C 21 MET cc_start: 0.8788 (mmm) cc_final: 0.7915 (ttt) REVERT: E 43 LYS cc_start: 0.8528 (mmtm) cc_final: 0.8292 (mptm) REVERT: E 145 SER cc_start: 0.8169 (m) cc_final: 0.7832 (p) REVERT: E 160 ARG cc_start: 0.7107 (ttp-110) cc_final: 0.6757 (ttp-110) REVERT: E 230 MET cc_start: 0.9132 (ttp) cc_final: 0.8765 (ttp) REVERT: R 173 MET cc_start: 0.6961 (tmm) cc_final: 0.6649 (tpt) REVERT: R 250 TYR cc_start: 0.8249 (m-10) cc_final: 0.7457 (m-10) REVERT: R 313 GLN cc_start: 0.7258 (tt0) cc_final: 0.7003 (tt0) REVERT: R 319 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6330 (ttp-170) REVERT: R 345 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6703 (mp10) outliers start: 24 outliers final: 19 residues processed: 165 average time/residue: 1.4562 time to fit residues: 253.3378 Evaluate side-chains 174 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 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 E residue 11 LEU Chi-restraints excluded: chain E residue 17 SER 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 E residue 186 GLN 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 Chi-restraints excluded: chain R residue 241 PHE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 319 ARG Chi-restraints excluded: chain R residue 345 GLN 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 41 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 83 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 255 ASN A 269 ASN A 346 ASN B 268 ASN E 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.170205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.118105 restraints weight = 10179.599| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.06 r_work: 0.3230 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9013 Z= 0.115 Angle : 0.490 7.581 12239 Z= 0.257 Chirality : 0.042 0.143 1406 Planarity : 0.003 0.048 1547 Dihedral : 4.103 41.677 1232 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.31 % Allowed : 16.49 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.25), residues: 1129 helix: 2.45 (0.26), residues: 403 sheet: 0.45 (0.30), residues: 272 loop : 0.22 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.016 0.001 PHE R 161 TYR 0.013 0.001 TYR E 190 ARG 0.010 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 459) hydrogen bonds : angle 4.52686 ( 1299) SS BOND : bond 0.00291 ( 3) SS BOND : angle 0.69957 ( 6) covalent geometry : bond 0.00255 ( 9010) covalent geometry : angle 0.49030 (12233) *********************** 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 174 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.978 Fit side-chains REVERT: A 29 LYS cc_start: 0.8165 (tttt) cc_final: 0.7629 (ttmm) REVERT: A 186 GLU cc_start: 0.8406 (tt0) cc_final: 0.7653 (tt0) REVERT: A 197 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8025 (mtpp) REVERT: A 208 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7449 (ttp80) REVERT: A 209 LYS cc_start: 0.8349 (pttt) cc_final: 0.8032 (ptmt) REVERT: A 330 LYS cc_start: 0.7609 (mttt) cc_final: 0.6971 (mtpt) REVERT: B 19 ARG cc_start: 0.6999 (ttp80) cc_final: 0.6628 (ttp80) REVERT: B 46 ARG cc_start: 0.8119 (mtp-110) cc_final: 0.7291 (mmt-90) REVERT: B 129 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7638 (mmt180) REVERT: B 226 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8033 (mp0) REVERT: C 21 MET cc_start: 0.8735 (mmm) cc_final: 0.7847 (ttt) REVERT: E 43 LYS cc_start: 0.8483 (mmtm) cc_final: 0.8235 (mptm) REVERT: E 145 SER cc_start: 0.8184 (m) cc_final: 0.7840 (p) REVERT: E 160 ARG cc_start: 0.7060 (ttp-110) cc_final: 0.6738 (ttp-110) REVERT: E 230 MET cc_start: 0.9119 (ttp) cc_final: 0.8742 (ttp) REVERT: R 173 MET cc_start: 0.7105 (tmm) cc_final: 0.6415 (tpt) REVERT: R 250 TYR cc_start: 0.8233 (m-10) cc_final: 0.7443 (m-10) REVERT: R 299 ARG cc_start: 0.7411 (mtp85) cc_final: 0.7098 (mmm-85) REVERT: R 313 GLN cc_start: 0.7204 (tt0) cc_final: 0.6982 (tt0) REVERT: R 319 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.6301 (ttp-170) outliers start: 22 outliers final: 19 residues processed: 162 average time/residue: 1.7372 time to fit residues: 296.8745 Evaluate side-chains 167 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 251 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 76 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 B residue 331 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 241 PHE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 319 ARG 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 58 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.170234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.118154 restraints weight = 10096.921| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.05 r_work: 0.3234 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9013 Z= 0.117 Angle : 0.510 13.333 12239 Z= 0.261 Chirality : 0.042 0.150 1406 Planarity : 0.004 0.049 1547 Dihedral : 4.067 40.473 1232 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.21 % Allowed : 16.81 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.25), residues: 1129 helix: 2.46 (0.26), residues: 403 sheet: 0.40 (0.30), residues: 277 loop : 0.26 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS A 188 PHE 0.015 0.001 PHE R 161 TYR 0.014 0.001 TYR E 190 ARG 0.010 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 459) hydrogen bonds : angle 4.50040 ( 1299) SS BOND : bond 0.00281 ( 3) SS BOND : angle 0.78742 ( 6) covalent geometry : bond 0.00263 ( 9010) covalent geometry : angle 0.50940 (12233) ********************** 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 167 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.003 Fit side-chains REVERT: A 29 LYS cc_start: 0.8145 (tttt) cc_final: 0.7627 (ttmm) REVERT: A 186 GLU cc_start: 0.8394 (tt0) cc_final: 0.7643 (tt0) REVERT: A 197 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7968 (mtpp) REVERT: A 208 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7461 (ttp80) REVERT: A 209 LYS cc_start: 0.8359 (pttt) cc_final: 0.8040 (ptmt) REVERT: A 255 ASN cc_start: 0.8506 (m-40) cc_final: 0.8286 (m110) REVERT: A 306 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7469 (mm-40) REVERT: A 330 LYS cc_start: 0.7615 (mttt) cc_final: 0.6985 (mtpt) REVERT: B 19 ARG cc_start: 0.7003 (ttp80) cc_final: 0.6636 (ttp80) REVERT: B 46 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7323 (mmt-90) REVERT: B 129 ARG cc_start: 0.8190 (mtp180) cc_final: 0.7644 (mmt180) REVERT: B 226 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8020 (mp0) REVERT: C 21 MET cc_start: 0.8736 (mmm) cc_final: 0.7843 (ttt) REVERT: E 43 LYS cc_start: 0.8486 (mmtm) cc_final: 0.8246 (mptm) REVERT: E 145 SER cc_start: 0.8187 (m) cc_final: 0.7841 (p) REVERT: E 160 ARG cc_start: 0.7038 (ttp-110) cc_final: 0.6759 (ttm110) REVERT: R 173 MET cc_start: 0.6993 (tmm) cc_final: 0.6702 (tpt) REVERT: R 250 TYR cc_start: 0.8235 (m-10) cc_final: 0.7438 (m-10) REVERT: R 299 ARG cc_start: 0.7345 (mtp85) cc_final: 0.6938 (mmm-85) REVERT: R 303 ARG cc_start: 0.7442 (mmm160) cc_final: 0.6878 (mmm-85) REVERT: R 313 GLN cc_start: 0.7215 (tt0) cc_final: 0.7003 (tt0) REVERT: R 319 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6304 (ttp-170) REVERT: R 386 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7849 (p) outliers start: 21 outliers final: 15 residues processed: 155 average time/residue: 1.6418 time to fit residues: 268.8279 Evaluate side-chains 159 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 38 ASP Chi-restraints excluded: chain B residue 76 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 B residue 331 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 241 PHE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 319 ARG 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 41 optimal weight: 0.0670 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 104 optimal weight: 0.0050 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 overall best weight: 0.4332 ------------------------------------------------------------------------------- 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 A 346 ASN B 32 GLN B 268 ASN E 194 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.171677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119944 restraints weight = 10167.734| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.06 r_work: 0.3248 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9013 Z= 0.098 Angle : 0.482 8.064 12239 Z= 0.251 Chirality : 0.042 0.150 1406 Planarity : 0.003 0.049 1547 Dihedral : 3.945 37.283 1232 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.00 % Allowed : 17.02 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1129 helix: 2.51 (0.26), residues: 401 sheet: 0.48 (0.30), residues: 269 loop : 0.26 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS A 188 PHE 0.014 0.001 PHE R 161 TYR 0.015 0.001 TYR E 190 ARG 0.009 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 459) hydrogen bonds : angle 4.40048 ( 1299) SS BOND : bond 0.00276 ( 3) SS BOND : angle 0.61358 ( 6) covalent geometry : bond 0.00210 ( 9010) covalent geometry : angle 0.48231 (12233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7828.04 seconds wall clock time: 136 minutes 55.54 seconds (8215.54 seconds total)