Starting phenix.real_space_refine on Mon May 12 05:13:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwj_37890/05_2025/8wwj_37890.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwj_37890/05_2025/8wwj_37890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wwj_37890/05_2025/8wwj_37890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwj_37890/05_2025/8wwj_37890.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwj_37890/05_2025/8wwj_37890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwj_37890/05_2025/8wwj_37890.cif" } resolution = 3.03 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= 0.054 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 Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.45, per 1000 atoms: 0.62 Number of scatterers: 8821 At special positions: 0 Unit cell: (87.74, 117.7, 126.26, 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: 2.32 Conformation dependent library (CDL) restraints added in 1.1 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 38.4% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.627A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.224A 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 270 through 281 removed outlier: 3.662A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.103A 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: 4.403A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 3 through 25 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: 3.577A 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: 3.950A pdb=" N MET R 184 " --> pdb=" O PHE R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 223 removed outlier: 3.584A pdb=" N THR R 221 " --> pdb=" O ILE R 218 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS R 222 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 244 Processing helix chain 'R' and resid 244 through 250 Processing helix chain 'R' and resid 269 through 286 removed outlier: 3.758A pdb=" N LEU R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR R 275 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 4.592A 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 337 removed outlier: 3.617A pdb=" N ALA R 329 " --> pdb=" O ARG R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 351 removed outlier: 4.037A pdb=" N LEU R 349 " --> pdb=" O GLN R 345 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 355 through 384 removed outlier: 4.287A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS R 374 " --> pdb=" O TYR R 370 " (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: 6.281A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.674A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.570A 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: 3.783A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.895A 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: 6.076A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.146A 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: 6.215A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.608A 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: 6.855A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.246A 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: 6.507A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.878A 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: 3.723A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.311A 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: 6.859A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.617A 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: 4.192A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.629A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 251 through 254 removed outlier: 3.546A pdb=" N ARG R 252 " --> pdb=" O GLY R 264 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY R 264 " --> pdb=" O ARG R 252 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1311 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: 2.64 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: 2842 1.34 - 1.46: 1806 1.46 - 1.58: 4269 1.58 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 9010 Sorted by residual: bond pdb=" CG1 ILE B 81 " pdb=" CD1 ILE B 81 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.13e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.475 0.023 3.10e-02 1.04e+03 5.70e-01 bond pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 1.513 1.486 0.027 3.90e-02 6.57e+02 4.68e-01 bond pdb=" CB ASP A 20 " pdb=" CG ASP A 20 " ideal model delta sigma weight residual 1.516 1.499 0.017 2.50e-02 1.60e+03 4.62e-01 bond pdb=" C LEU B 336 " pdb=" N LYS B 337 " ideal model delta sigma weight residual 1.331 1.321 0.010 1.55e-02 4.16e+03 4.28e-01 ... (remaining 9005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 11919 1.09 - 2.18: 252 2.18 - 3.26: 42 3.26 - 4.35: 9 4.35 - 5.44: 11 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 121.54 125.78 -4.24 1.91e+00 2.74e-01 4.94e+00 angle pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" C TYR E 102 " ideal model delta sigma weight residual 108.96 106.16 2.80 1.49e+00 4.50e-01 3.52e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 124.31 127.18 -2.87 1.67e+00 3.59e-01 2.95e+00 angle pdb=" CA TYR E 103 " pdb=" CB TYR E 103 " pdb=" CG TYR E 103 " ideal model delta sigma weight residual 113.90 110.85 3.05 1.80e+00 3.09e-01 2.88e+00 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 123.93 126.49 -2.56 1.54e+00 4.22e-01 2.76e+00 ... (remaining 12228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 5148 16.41 - 32.83: 145 32.83 - 49.24: 33 49.24 - 65.66: 4 65.66 - 82.07: 1 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 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+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 180.00 161.36 18.64 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 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 814 0.028 - 0.055: 372 0.055 - 0.083: 126 0.083 - 0.110: 73 0.110 - 0.138: 21 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CA ILE A 221 " pdb=" N ILE A 221 " pdb=" C ILE A 221 " pdb=" CB ILE A 221 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA THR B 164 " pdb=" N THR B 164 " pdb=" C THR B 164 " pdb=" CB THR B 164 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 1403 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 236 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO B 194 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 151 " -0.010 2.00e-02 2.50e+03 7.30e-03 9.32e-01 pdb=" CG PHE B 151 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE B 151 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 151 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 151 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 151 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 151 " -0.003 2.00e-02 2.50e+03 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 138 2.67 - 3.23: 8324 3.23 - 3.79: 13871 3.79 - 4.34: 19515 4.34 - 4.90: 32609 Nonbonded interactions: 74457 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.118 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.119 3.040 nonbonded pdb=" O SER R 243 " pdb=" OH TYR R 280 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.227 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.271 3.040 ... (remaining 74452 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.530 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 0.041 9013 Z= 0.138 Angle : 0.435 5.439 12239 Z= 0.230 Chirality : 0.041 0.138 1406 Planarity : 0.003 0.045 1547 Dihedral : 8.315 82.072 3182 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.63 % Allowed : 2.63 % Favored : 96.74 % 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: 1.11 (0.25), residues: 1129 helix: 1.24 (0.26), residues: 394 sheet: 0.77 (0.29), residues: 291 loop : 0.44 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.002 0.001 HIS E 35 PHE 0.016 0.001 PHE B 151 TYR 0.013 0.001 TYR E 190 ARG 0.002 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.24674 ( 461) hydrogen bonds : angle 7.49302 ( 1311) SS BOND : bond 0.00167 ( 3) SS BOND : angle 0.54142 ( 6) covalent geometry : bond 0.00327 ( 9010) covalent geometry : angle 0.43494 (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 262 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 256 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8562 (mmm) cc_final: 0.8336 (mmm) REVERT: A 290 TYR cc_start: 0.8615 (t80) cc_final: 0.8302 (t80) REVERT: A 314 LYS cc_start: 0.7632 (mttt) cc_final: 0.7338 (mtpt) REVERT: B 19 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7614 (ttp80) REVERT: B 57 LYS cc_start: 0.8581 (mppt) cc_final: 0.8211 (mtmt) REVERT: B 186 ASP cc_start: 0.8597 (m-30) cc_final: 0.8327 (m-30) REVERT: B 214 ARG cc_start: 0.7856 (mmt180) cc_final: 0.7598 (mmt180) REVERT: B 333 ASP cc_start: 0.8531 (p0) cc_final: 0.8281 (p0) REVERT: C 17 GLU cc_start: 0.8599 (tp30) cc_final: 0.8389 (tp30) REVERT: C 38 MET cc_start: 0.7048 (ttp) cc_final: 0.6564 (tpt) REVERT: E 46 GLU cc_start: 0.7824 (tt0) cc_final: 0.7310 (tt0) REVERT: E 83 MET cc_start: 0.8259 (mtm) cc_final: 0.8003 (mtm) REVERT: E 85 SER cc_start: 0.9066 (m) cc_final: 0.8804 (p) REVERT: E 160 ARG cc_start: 0.7391 (mtp-110) cc_final: 0.6832 (ttm-80) REVERT: E 186 GLN cc_start: 0.8114 (tt0) cc_final: 0.7718 (tt0) REVERT: E 213 THR cc_start: 0.8269 (m) cc_final: 0.8035 (p) REVERT: E 215 THR cc_start: 0.7716 (m) cc_final: 0.7326 (t) REVERT: E 217 SER cc_start: 0.8255 (m) cc_final: 0.7821 (t) outliers start: 6 outliers final: 2 residues processed: 260 average time/residue: 0.2545 time to fit residues: 85.6422 Evaluate side-chains 188 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 192 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: 1.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 91 HIS B 259 GLN E 171 ASN E 179 GLN R 194 ASN R 216 HIS R 281 GLN R 345 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.186094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.134127 restraints weight = 10775.284| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.40 r_work: 0.3438 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.004 0.040 9013 Z= 0.160 Angle : 0.555 6.365 12239 Z= 0.300 Chirality : 0.043 0.151 1406 Planarity : 0.004 0.043 1547 Dihedral : 4.558 52.940 1236 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.21 % Allowed : 11.03 % Favored : 86.76 % 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: 1.47 (0.25), residues: 1129 helix: 2.10 (0.26), residues: 395 sheet: 0.73 (0.29), residues: 299 loop : 0.21 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 248 HIS 0.003 0.001 HIS R 216 PHE 0.016 0.001 PHE B 151 TYR 0.018 0.002 TYR E 190 ARG 0.004 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.05281 ( 461) hydrogen bonds : angle 5.15461 ( 1311) SS BOND : bond 0.00262 ( 3) SS BOND : angle 0.95768 ( 6) covalent geometry : bond 0.00354 ( 9010) covalent geometry : angle 0.55517 (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 224 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 TYR cc_start: 0.8569 (t80) cc_final: 0.8301 (t80) REVERT: A 314 LYS cc_start: 0.7827 (mttt) cc_final: 0.7406 (mtpt) REVERT: B 19 ARG cc_start: 0.8018 (ttp80) cc_final: 0.7670 (ttp80) REVERT: B 57 LYS cc_start: 0.8601 (mppt) cc_final: 0.8399 (mtpt) REVERT: B 170 ASP cc_start: 0.8578 (t70) cc_final: 0.8264 (t0) REVERT: B 186 ASP cc_start: 0.8751 (m-30) cc_final: 0.8377 (m-30) REVERT: B 188 MET cc_start: 0.8704 (mmm) cc_final: 0.8006 (mmp) REVERT: B 214 ARG cc_start: 0.8299 (mmt180) cc_final: 0.7949 (mmt180) REVERT: B 277 SER cc_start: 0.8131 (t) cc_final: 0.7847 (m) REVERT: B 303 ASP cc_start: 0.7566 (m-30) cc_final: 0.7270 (m-30) REVERT: C 15 LEU cc_start: 0.9151 (mm) cc_final: 0.8846 (tt) REVERT: C 17 GLU cc_start: 0.8988 (tp30) cc_final: 0.8587 (tp30) REVERT: C 32 LYS cc_start: 0.8197 (tppt) cc_final: 0.7855 (tttt) REVERT: C 38 MET cc_start: 0.7134 (ttp) cc_final: 0.6441 (tpt) REVERT: E 46 GLU cc_start: 0.8264 (tt0) cc_final: 0.7685 (tt0) REVERT: E 83 MET cc_start: 0.8220 (mtm) cc_final: 0.8009 (mtm) REVERT: E 160 ARG cc_start: 0.7712 (mtp-110) cc_final: 0.6923 (ttm-80) REVERT: E 186 GLN cc_start: 0.8459 (tt0) cc_final: 0.8068 (tt0) REVERT: E 224 VAL cc_start: 0.7452 (t) cc_final: 0.7246 (p) REVERT: R 169 ILE cc_start: 0.7629 (pt) cc_final: 0.7112 (pp) REVERT: R 303 ARG cc_start: 0.7416 (mtp85) cc_final: 0.7208 (mtp85) REVERT: R 342 TYR cc_start: 0.7925 (m-80) cc_final: 0.7535 (m-80) REVERT: R 380 TYR cc_start: 0.7946 (t80) cc_final: 0.7714 (t80) REVERT: R 388 ARG cc_start: 0.7753 (ttp-170) cc_final: 0.7238 (ttp-110) outliers start: 21 outliers final: 10 residues processed: 214 average time/residue: 0.2622 time to fit residues: 73.3172 Evaluate side-chains 189 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 179 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 343 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN E 179 GLN R 179 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.183789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132914 restraints weight = 10913.293| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.34 r_work: 0.3412 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9013 Z= 0.196 Angle : 0.562 6.817 12239 Z= 0.298 Chirality : 0.044 0.150 1406 Planarity : 0.004 0.042 1547 Dihedral : 4.234 28.353 1232 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.15 % Allowed : 12.61 % Favored : 84.24 % 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: 1.31 (0.25), residues: 1129 helix: 2.11 (0.26), residues: 395 sheet: 0.39 (0.29), residues: 304 loop : 0.17 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.004 0.001 HIS A 188 PHE 0.033 0.002 PHE R 387 TYR 0.035 0.002 TYR R 360 ARG 0.006 0.001 ARG R 322 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 461) hydrogen bonds : angle 4.93961 ( 1311) SS BOND : bond 0.00275 ( 3) SS BOND : angle 0.95962 ( 6) covalent geometry : bond 0.00460 ( 9010) covalent geometry : angle 0.56132 (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 215 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8154 (ttm) cc_final: 0.7783 (ttm) REVERT: A 244 HIS cc_start: 0.8185 (m90) cc_final: 0.7883 (m-70) REVERT: A 290 TYR cc_start: 0.8636 (t80) cc_final: 0.8262 (t80) REVERT: A 314 LYS cc_start: 0.7929 (mttt) cc_final: 0.7615 (mtpt) REVERT: B 13 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8218 (pp30) REVERT: B 19 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7770 (ttp80) REVERT: B 57 LYS cc_start: 0.8640 (mppt) cc_final: 0.8384 (mtpt) REVERT: B 170 ASP cc_start: 0.8568 (t70) cc_final: 0.8270 (t0) REVERT: B 186 ASP cc_start: 0.8858 (m-30) cc_final: 0.8554 (m-30) REVERT: B 217 MET cc_start: 0.8043 (ptm) cc_final: 0.7461 (ptm) REVERT: B 277 SER cc_start: 0.8198 (t) cc_final: 0.7908 (m) REVERT: B 303 ASP cc_start: 0.7714 (m-30) cc_final: 0.7386 (m-30) REVERT: C 17 GLU cc_start: 0.8967 (tp30) cc_final: 0.8692 (tp30) REVERT: C 38 MET cc_start: 0.7196 (ttp) cc_final: 0.6892 (ttp) REVERT: E 46 GLU cc_start: 0.8215 (tt0) cc_final: 0.7654 (tt0) REVERT: E 142 GLN cc_start: 0.6884 (mt0) cc_final: 0.6140 (mt0) REVERT: E 160 ARG cc_start: 0.7936 (mtp-110) cc_final: 0.7251 (ttm-80) REVERT: E 186 GLN cc_start: 0.8519 (tt0) cc_final: 0.8129 (tt0) REVERT: E 224 VAL cc_start: 0.7515 (t) cc_final: 0.7298 (p) REVERT: E 234 GLU cc_start: 0.8471 (tp30) cc_final: 0.8162 (tp30) REVERT: R 278 THR cc_start: 0.8677 (m) cc_final: 0.8456 (t) REVERT: R 325 ARG cc_start: 0.8450 (ptp90) cc_final: 0.7967 (ttp80) REVERT: R 342 TYR cc_start: 0.8402 (m-80) cc_final: 0.7912 (m-80) REVERT: R 388 ARG cc_start: 0.7717 (ttp-170) cc_final: 0.7362 (ttp-110) outliers start: 30 outliers final: 22 residues processed: 197 average time/residue: 0.2618 time to fit residues: 66.8755 Evaluate side-chains 199 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain R residue 372 ASN Chi-restraints excluded: chain R residue 379 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.185808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.136225 restraints weight = 10870.683| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.67 r_work: 0.3418 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2820 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= 0.135 Angle : 0.512 6.298 12239 Z= 0.272 Chirality : 0.042 0.140 1406 Planarity : 0.003 0.041 1547 Dihedral : 4.068 29.214 1232 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.52 % Allowed : 14.08 % Favored : 83.40 % 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: 1.36 (0.25), residues: 1129 helix: 2.26 (0.26), residues: 396 sheet: 0.43 (0.30), residues: 286 loop : 0.07 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.021 0.001 PHE R 387 TYR 0.038 0.002 TYR R 360 ARG 0.006 0.000 ARG R 322 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 461) hydrogen bonds : angle 4.73334 ( 1311) SS BOND : bond 0.00220 ( 3) SS BOND : angle 1.83721 ( 6) covalent geometry : bond 0.00304 ( 9010) covalent geometry : angle 0.51018 (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 202 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7404 (ttm) REVERT: A 186 GLU cc_start: 0.8118 (tt0) cc_final: 0.7890 (tt0) REVERT: A 197 LYS cc_start: 0.8275 (mtmt) cc_final: 0.7813 (mttp) REVERT: A 290 TYR cc_start: 0.8631 (t80) cc_final: 0.8248 (t80) REVERT: A 314 LYS cc_start: 0.7840 (mttt) cc_final: 0.7533 (mtpt) REVERT: B 13 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8210 (pp30) REVERT: B 19 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7740 (ttp80) REVERT: B 36 ASN cc_start: 0.8563 (m-40) cc_final: 0.8299 (p0) REVERT: B 57 LYS cc_start: 0.8496 (mppt) cc_final: 0.8265 (mtpt) REVERT: B 170 ASP cc_start: 0.8438 (t70) cc_final: 0.8213 (t0) REVERT: B 186 ASP cc_start: 0.8731 (m-30) cc_final: 0.8474 (m-30) REVERT: B 277 SER cc_start: 0.7973 (t) cc_final: 0.7724 (m) REVERT: B 303 ASP cc_start: 0.7412 (m-30) cc_final: 0.7083 (m-30) REVERT: C 17 GLU cc_start: 0.8893 (tp30) cc_final: 0.8604 (tp30) REVERT: E 46 GLU cc_start: 0.8035 (tt0) cc_final: 0.7422 (tt0) REVERT: E 160 ARG cc_start: 0.7911 (mtp-110) cc_final: 0.7253 (ttm-80) REVERT: E 224 VAL cc_start: 0.7542 (t) cc_final: 0.7336 (p) REVERT: E 234 GLU cc_start: 0.8282 (tp30) cc_final: 0.7885 (tp30) REVERT: R 303 ARG cc_start: 0.7531 (mtp85) cc_final: 0.7272 (mtp85) REVERT: R 342 TYR cc_start: 0.8397 (m-80) cc_final: 0.7896 (m-80) REVERT: R 388 ARG cc_start: 0.7653 (ttp-170) cc_final: 0.7266 (ttp-110) outliers start: 24 outliers final: 18 residues processed: 188 average time/residue: 0.2604 time to fit residues: 63.5484 Evaluate side-chains 191 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain R residue 379 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 78 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.186250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136686 restraints weight = 10862.686| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.66 r_work: 0.3421 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9013 Z= 0.134 Angle : 0.507 5.460 12239 Z= 0.270 Chirality : 0.042 0.137 1406 Planarity : 0.003 0.040 1547 Dihedral : 4.007 29.344 1232 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.73 % Allowed : 14.29 % Favored : 82.98 % 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: 2.30 (0.26), residues: 396 sheet: 0.30 (0.29), residues: 303 loop : 0.15 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.033 0.001 PHE R 387 TYR 0.038 0.002 TYR R 360 ARG 0.006 0.000 ARG R 322 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 461) hydrogen bonds : angle 4.62981 ( 1311) SS BOND : bond 0.00194 ( 3) SS BOND : angle 1.09989 ( 6) covalent geometry : bond 0.00307 ( 9010) covalent geometry : angle 0.50687 (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 202 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7494 (ttm) REVERT: A 29 LYS cc_start: 0.8360 (ttpp) cc_final: 0.8143 (tttm) REVERT: A 186 GLU cc_start: 0.8155 (tt0) cc_final: 0.7859 (tt0) REVERT: A 197 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7842 (mttp) REVERT: A 290 TYR cc_start: 0.8639 (t80) cc_final: 0.8271 (t80) REVERT: A 314 LYS cc_start: 0.7867 (mttt) cc_final: 0.7557 (mtpt) REVERT: B 13 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8268 (pp30) REVERT: B 19 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7731 (ttp80) REVERT: B 170 ASP cc_start: 0.8395 (t70) cc_final: 0.8181 (t0) REVERT: B 186 ASP cc_start: 0.8776 (m-30) cc_final: 0.8496 (m-30) REVERT: B 264 TYR cc_start: 0.7936 (m-80) cc_final: 0.7157 (m-80) REVERT: B 277 SER cc_start: 0.7978 (t) cc_final: 0.7736 (m) REVERT: B 303 ASP cc_start: 0.7679 (m-30) cc_final: 0.7291 (m-30) REVERT: B 331 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.9054 (p) REVERT: E 46 GLU cc_start: 0.8028 (tt0) cc_final: 0.7449 (tt0) REVERT: E 83 MET cc_start: 0.7990 (mtm) cc_final: 0.7784 (mtm) REVERT: E 160 ARG cc_start: 0.7901 (mtp-110) cc_final: 0.7239 (ttm-80) REVERT: E 175 TYR cc_start: 0.8481 (m-80) cc_final: 0.8273 (m-80) REVERT: E 215 THR cc_start: 0.7750 (m) cc_final: 0.7443 (t) REVERT: E 224 VAL cc_start: 0.7529 (t) cc_final: 0.7326 (p) REVERT: E 234 GLU cc_start: 0.8284 (tp30) cc_final: 0.7866 (tp30) REVERT: R 280 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6712 (t80) REVERT: R 325 ARG cc_start: 0.8371 (ptp90) cc_final: 0.7856 (ttp80) REVERT: R 342 TYR cc_start: 0.8423 (m-80) cc_final: 0.7917 (m-80) REVERT: R 380 TYR cc_start: 0.8405 (t80) cc_final: 0.7807 (t80) REVERT: R 388 ARG cc_start: 0.7625 (ttp-170) cc_final: 0.7239 (ttp-110) outliers start: 26 outliers final: 21 residues processed: 187 average time/residue: 0.2945 time to fit residues: 71.0781 Evaluate side-chains 198 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 372 ASN Chi-restraints excluded: chain R residue 379 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.188394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144435 restraints weight = 10638.247| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.52 r_work: 0.3474 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9013 Z= 0.136 Angle : 0.500 5.345 12239 Z= 0.267 Chirality : 0.042 0.137 1406 Planarity : 0.003 0.040 1547 Dihedral : 3.978 29.553 1232 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.42 % Allowed : 14.50 % Favored : 83.09 % 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: 1.40 (0.25), residues: 1129 helix: 2.29 (0.26), residues: 398 sheet: 0.31 (0.30), residues: 296 loop : 0.19 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.031 0.001 PHE R 387 TYR 0.040 0.001 TYR R 360 ARG 0.006 0.000 ARG R 322 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 461) hydrogen bonds : angle 4.54748 ( 1311) SS BOND : bond 0.00167 ( 3) SS BOND : angle 0.98222 ( 6) covalent geometry : bond 0.00312 ( 9010) covalent geometry : angle 0.49984 (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 200 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7606 (ttm) REVERT: A 186 GLU cc_start: 0.8032 (tt0) cc_final: 0.7777 (tt0) REVERT: A 197 LYS cc_start: 0.8343 (mtmt) cc_final: 0.7977 (mtmt) REVERT: A 290 TYR cc_start: 0.8664 (t80) cc_final: 0.8275 (t80) REVERT: A 314 LYS cc_start: 0.7955 (mttt) cc_final: 0.7670 (mtpt) REVERT: B 13 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8309 (pp30) REVERT: B 19 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7808 (ttp80) REVERT: B 186 ASP cc_start: 0.8694 (m-30) cc_final: 0.8446 (m-30) REVERT: B 217 MET cc_start: 0.7972 (ptm) cc_final: 0.7322 (ptm) REVERT: B 264 TYR cc_start: 0.8023 (m-80) cc_final: 0.7292 (m-80) REVERT: B 303 ASP cc_start: 0.7672 (m-30) cc_final: 0.7263 (m-30) REVERT: E 46 GLU cc_start: 0.8016 (tt0) cc_final: 0.7519 (tt0) REVERT: E 160 ARG cc_start: 0.7872 (mtp-110) cc_final: 0.7311 (ttm-80) REVERT: E 175 TYR cc_start: 0.8487 (m-80) cc_final: 0.8250 (m-80) REVERT: E 186 GLN cc_start: 0.8213 (tt0) cc_final: 0.7987 (pt0) REVERT: E 234 GLU cc_start: 0.8272 (tp30) cc_final: 0.7867 (tp30) REVERT: R 280 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.6657 (t80) REVERT: R 342 TYR cc_start: 0.8410 (m-80) cc_final: 0.8013 (m-80) REVERT: R 380 TYR cc_start: 0.8456 (t80) cc_final: 0.7960 (t80) REVERT: R 388 ARG cc_start: 0.7529 (ttp-170) cc_final: 0.7169 (ttp-110) outliers start: 23 outliers final: 19 residues processed: 186 average time/residue: 0.2590 time to fit residues: 62.8699 Evaluate side-chains 191 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 372 ASN Chi-restraints excluded: chain R residue 379 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 0.9990 chunk 60 optimal weight: 0.0670 chunk 9 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN E 194 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 = 0.4230 r_free = 0.4230 target = 0.189909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141732 restraints weight = 10810.263| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.61 r_work: 0.3516 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9013 Z= 0.121 Angle : 0.496 5.582 12239 Z= 0.264 Chirality : 0.041 0.134 1406 Planarity : 0.003 0.039 1547 Dihedral : 3.930 29.677 1232 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.52 % Allowed : 14.92 % 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 (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: 1.45 (0.26), residues: 1129 helix: 2.35 (0.26), residues: 398 sheet: 0.37 (0.30), residues: 294 loop : 0.17 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.034 0.001 PHE R 387 TYR 0.039 0.001 TYR R 360 ARG 0.006 0.000 ARG R 322 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 461) hydrogen bonds : angle 4.49844 ( 1311) SS BOND : bond 0.00165 ( 3) SS BOND : angle 0.77352 ( 6) covalent geometry : bond 0.00273 ( 9010) covalent geometry : angle 0.49580 (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 198 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8383 (tttm) cc_final: 0.7755 (tptp) REVERT: A 186 GLU cc_start: 0.8211 (tt0) cc_final: 0.7938 (tt0) REVERT: A 197 LYS cc_start: 0.8616 (mtmt) cc_final: 0.8239 (mtmt) REVERT: A 290 TYR cc_start: 0.8642 (t80) cc_final: 0.8244 (t80) REVERT: A 314 LYS cc_start: 0.7969 (mttt) cc_final: 0.7647 (mtpt) REVERT: B 13 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8289 (pp30) REVERT: B 19 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7807 (ttp80) REVERT: B 186 ASP cc_start: 0.8700 (m-30) cc_final: 0.8359 (m-30) REVERT: B 264 TYR cc_start: 0.8033 (m-80) cc_final: 0.7356 (m-80) REVERT: B 303 ASP cc_start: 0.7797 (m-30) cc_final: 0.7366 (m-30) REVERT: C 28 ILE cc_start: 0.8919 (pt) cc_final: 0.8691 (tp) REVERT: E 46 GLU cc_start: 0.8024 (tt0) cc_final: 0.7511 (tt0) REVERT: E 83 MET cc_start: 0.8032 (mtm) cc_final: 0.7808 (mtm) REVERT: E 160 ARG cc_start: 0.7886 (mtp-110) cc_final: 0.7160 (ttm-80) REVERT: E 175 TYR cc_start: 0.8501 (m-80) cc_final: 0.8258 (m-80) REVERT: E 186 GLN cc_start: 0.8344 (tt0) cc_final: 0.8107 (pt0) REVERT: E 234 GLU cc_start: 0.8445 (tp30) cc_final: 0.7963 (tp30) REVERT: R 180 PHE cc_start: 0.7870 (m-10) cc_final: 0.7608 (t80) REVERT: R 250 TYR cc_start: 0.8226 (m-80) cc_final: 0.7994 (m-80) REVERT: R 280 TYR cc_start: 0.7365 (OUTLIER) cc_final: 0.6580 (t80) REVERT: R 342 TYR cc_start: 0.8511 (m-80) cc_final: 0.8058 (m-80) REVERT: R 380 TYR cc_start: 0.8474 (t80) cc_final: 0.7969 (t80) REVERT: R 388 ARG cc_start: 0.7564 (ttp-170) cc_final: 0.7133 (ttp-110) outliers start: 24 outliers final: 19 residues processed: 186 average time/residue: 0.2452 time to fit residues: 59.7067 Evaluate side-chains 186 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 372 ASN Chi-restraints excluded: chain R residue 379 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.187789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135894 restraints weight = 10880.067| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.39 r_work: 0.3487 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9013 Z= 0.171 Angle : 0.533 6.237 12239 Z= 0.284 Chirality : 0.043 0.144 1406 Planarity : 0.004 0.039 1547 Dihedral : 4.063 30.774 1232 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.84 % Allowed : 14.81 % 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 (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: 1.35 (0.26), residues: 1129 helix: 2.31 (0.27), residues: 398 sheet: 0.23 (0.30), residues: 296 loop : 0.14 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 339 HIS 0.004 0.001 HIS E 35 PHE 0.029 0.002 PHE R 387 TYR 0.042 0.002 TYR R 360 ARG 0.006 0.001 ARG R 322 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 461) hydrogen bonds : angle 4.59773 ( 1311) SS BOND : bond 0.00174 ( 3) SS BOND : angle 0.92127 ( 6) covalent geometry : bond 0.00399 ( 9010) covalent geometry : angle 0.53258 (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 195 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8418 (tttm) cc_final: 0.7830 (tptp) REVERT: A 186 GLU cc_start: 0.8288 (tt0) cc_final: 0.7988 (tt0) REVERT: A 197 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8292 (mtmt) REVERT: A 290 TYR cc_start: 0.8668 (t80) cc_final: 0.8267 (t80) REVERT: A 314 LYS cc_start: 0.7986 (mttt) cc_final: 0.7662 (mtpt) REVERT: B 13 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8276 (pp30) REVERT: B 19 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7821 (ttp80) REVERT: B 186 ASP cc_start: 0.8793 (m-30) cc_final: 0.8483 (m-30) REVERT: B 217 MET cc_start: 0.8062 (ptm) cc_final: 0.7327 (ptm) REVERT: B 264 TYR cc_start: 0.8069 (m-80) cc_final: 0.7387 (m-80) REVERT: B 303 ASP cc_start: 0.7890 (m-30) cc_final: 0.7427 (m-30) REVERT: C 28 ILE cc_start: 0.8940 (pt) cc_final: 0.8690 (tp) REVERT: E 46 GLU cc_start: 0.8060 (tt0) cc_final: 0.7571 (tt0) REVERT: E 142 GLN cc_start: 0.7354 (mt0) cc_final: 0.7058 (mt0) REVERT: E 160 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.7185 (ttm-80) REVERT: E 175 TYR cc_start: 0.8493 (m-80) cc_final: 0.8232 (m-80) REVERT: E 186 GLN cc_start: 0.8327 (tt0) cc_final: 0.8086 (pt0) REVERT: E 218 ARG cc_start: 0.6828 (ttp-170) cc_final: 0.6578 (ttp-170) REVERT: R 280 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6599 (t80) REVERT: R 303 ARG cc_start: 0.7681 (mtp-110) cc_final: 0.7304 (mtp85) REVERT: R 342 TYR cc_start: 0.8494 (m-80) cc_final: 0.8076 (m-80) REVERT: R 380 TYR cc_start: 0.8480 (t80) cc_final: 0.8031 (t80) REVERT: R 388 ARG cc_start: 0.7572 (ttp-170) cc_final: 0.7161 (ttp-110) outliers start: 27 outliers final: 24 residues processed: 183 average time/residue: 0.2518 time to fit residues: 60.2787 Evaluate side-chains 190 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 372 ASN Chi-restraints excluded: chain R residue 379 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 95 optimal weight: 0.0980 chunk 75 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.190538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.147646 restraints weight = 10703.052| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.52 r_work: 0.3502 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3479 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= 0.105 Angle : 0.508 6.990 12239 Z= 0.267 Chirality : 0.041 0.137 1406 Planarity : 0.003 0.039 1547 Dihedral : 3.889 29.424 1232 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.31 % Allowed : 15.76 % Favored : 81.93 % 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: 1.45 (0.26), residues: 1129 helix: 2.40 (0.27), residues: 398 sheet: 0.36 (0.31), residues: 281 loop : 0.15 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.028 0.001 PHE R 387 TYR 0.041 0.001 TYR R 360 ARG 0.007 0.000 ARG R 322 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 461) hydrogen bonds : angle 4.45121 ( 1311) SS BOND : bond 0.00199 ( 3) SS BOND : angle 0.79874 ( 6) covalent geometry : bond 0.00229 ( 9010) covalent geometry : angle 0.50734 (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 194 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8031 (tt0) cc_final: 0.7751 (tt0) REVERT: A 197 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8258 (mtmt) REVERT: A 290 TYR cc_start: 0.8671 (t80) cc_final: 0.8279 (t80) REVERT: A 314 LYS cc_start: 0.7964 (mttt) cc_final: 0.7681 (mtpt) REVERT: B 19 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7779 (ttp80) REVERT: B 175 GLN cc_start: 0.8261 (mm-40) cc_final: 0.8045 (pt0) REVERT: B 186 ASP cc_start: 0.8604 (m-30) cc_final: 0.8371 (m-30) REVERT: B 217 MET cc_start: 0.7878 (ptm) cc_final: 0.7201 (ptm) REVERT: B 264 TYR cc_start: 0.7993 (m-80) cc_final: 0.7336 (m-80) REVERT: B 303 ASP cc_start: 0.7640 (m-30) cc_final: 0.7220 (m-30) REVERT: E 46 GLU cc_start: 0.7923 (tt0) cc_final: 0.7452 (tt0) REVERT: E 160 ARG cc_start: 0.7874 (mtp-110) cc_final: 0.7277 (ttm-80) REVERT: E 175 TYR cc_start: 0.8432 (m-80) cc_final: 0.8158 (m-80) REVERT: E 186 GLN cc_start: 0.8188 (tt0) cc_final: 0.7985 (pt0) REVERT: E 234 GLU cc_start: 0.8241 (tp30) cc_final: 0.7829 (tp30) REVERT: R 185 CYS cc_start: 0.5372 (OUTLIER) cc_final: 0.4458 (t) REVERT: R 280 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6743 (t80) REVERT: R 342 TYR cc_start: 0.8370 (m-80) cc_final: 0.8024 (m-80) REVERT: R 380 TYR cc_start: 0.8404 (t80) cc_final: 0.8020 (t80) REVERT: R 388 ARG cc_start: 0.7501 (ttp-170) cc_final: 0.7157 (ttp-110) outliers start: 22 outliers final: 15 residues processed: 183 average time/residue: 0.2626 time to fit residues: 63.4457 Evaluate side-chains 179 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.187568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145436 restraints weight = 10615.528| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.40 r_work: 0.3494 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9013 Z= 0.125 Angle : 0.530 7.499 12239 Z= 0.278 Chirality : 0.042 0.153 1406 Planarity : 0.004 0.039 1547 Dihedral : 3.923 29.301 1232 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.21 % Allowed : 16.39 % 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: 1.41 (0.26), residues: 1129 helix: 2.42 (0.26), residues: 396 sheet: 0.32 (0.30), residues: 293 loop : 0.09 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 PHE 0.029 0.001 PHE R 358 TYR 0.042 0.002 TYR R 360 ARG 0.009 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 461) hydrogen bonds : angle 4.44940 ( 1311) SS BOND : bond 0.00174 ( 3) SS BOND : angle 0.81563 ( 6) covalent geometry : bond 0.00284 ( 9010) covalent geometry : angle 0.53014 (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 186 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8040 (tt0) cc_final: 0.7743 (tt0) REVERT: A 197 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8246 (mtmt) REVERT: A 290 TYR cc_start: 0.8666 (t80) cc_final: 0.8378 (t80) REVERT: A 314 LYS cc_start: 0.7937 (mttt) cc_final: 0.7645 (mtpt) REVERT: B 19 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7789 (ttp80) REVERT: B 175 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8035 (pt0) REVERT: B 186 ASP cc_start: 0.8583 (m-30) cc_final: 0.8307 (m-30) REVERT: B 217 MET cc_start: 0.7928 (ptm) cc_final: 0.7211 (ptm) REVERT: B 264 TYR cc_start: 0.7992 (m-80) cc_final: 0.7307 (m-80) REVERT: B 303 ASP cc_start: 0.7703 (m-30) cc_final: 0.7276 (m-30) REVERT: E 46 GLU cc_start: 0.7860 (tt0) cc_final: 0.7386 (tt0) REVERT: E 160 ARG cc_start: 0.7896 (mtp-110) cc_final: 0.7239 (ttm-80) REVERT: E 175 TYR cc_start: 0.8473 (m-80) cc_final: 0.8145 (m-80) REVERT: E 186 GLN cc_start: 0.8181 (tt0) cc_final: 0.7950 (pt0) REVERT: E 234 GLU cc_start: 0.8236 (tp30) cc_final: 0.7788 (tp30) REVERT: R 185 CYS cc_start: 0.5556 (OUTLIER) cc_final: 0.4587 (t) REVERT: R 342 TYR cc_start: 0.8368 (m-80) cc_final: 0.7993 (m-80) REVERT: R 380 TYR cc_start: 0.8387 (t80) cc_final: 0.7998 (t80) REVERT: R 388 ARG cc_start: 0.7546 (ttp-170) cc_final: 0.7178 (ttp-110) outliers start: 21 outliers final: 15 residues processed: 174 average time/residue: 0.2577 time to fit residues: 59.2511 Evaluate side-chains 179 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 chunk 90 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN E 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.188550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.146831 restraints weight = 10668.277| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.38 r_work: 0.3508 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9013 Z= 0.111 Angle : 0.516 7.542 12239 Z= 0.271 Chirality : 0.041 0.140 1406 Planarity : 0.004 0.042 1547 Dihedral : 3.878 28.821 1232 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.00 % Allowed : 16.81 % 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: 1.42 (0.26), residues: 1129 helix: 2.45 (0.26), residues: 396 sheet: 0.32 (0.30), residues: 293 loop : 0.08 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.029 0.001 PHE R 358 TYR 0.043 0.002 TYR R 360 ARG 0.008 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 461) hydrogen bonds : angle 4.39529 ( 1311) SS BOND : bond 0.00196 ( 3) SS BOND : angle 0.72271 ( 6) covalent geometry : bond 0.00249 ( 9010) covalent geometry : angle 0.51547 (12233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5333.49 seconds wall clock time: 92 minutes 53.86 seconds (5573.86 seconds total)