Starting phenix.real_space_refine on Fri Oct 10 19:39:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwj_37890/10_2025/8wwj_37890.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwj_37890/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wwj_37890/10_2025/8wwj_37890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwj_37890/10_2025/8wwj_37890.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wwj_37890/10_2025/8wwj_37890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwj_37890/10_2025/8wwj_37890.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.054 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8821 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2235 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 2.06, per 1000 atoms: 0.23 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: 0.84 Conformation dependent library (CDL) restraints added in 297.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 38.4% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 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: 1.30 Time building geometry restraints manager: 1.11 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.660 ------------------------------------------------------------------------------- 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 : 5.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (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 ARG 0.002 0.000 ARG A 21 TYR 0.013 0.001 TYR E 190 PHE 0.016 0.001 PHE B 151 TRP 0.011 0.001 TRP B 99 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9010) covalent geometry : angle 0.43494 (12233) SS BOND : bond 0.00167 ( 3) SS BOND : angle 0.54142 ( 6) hydrogen bonds : bond 0.24674 ( 461) hydrogen bonds : angle 7.49302 ( 1311) *********************** 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 : 0.339 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: 0.7550 (ttp80) REVERT: B 23 LYS cc_start: 0.7625 (ttmm) cc_final: 0.7415 (mmmt) 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: 0.1249 time to fit residues: 41.8984 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 : 0.244 ------------------------------------------------------------------------------- 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 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 179 HIS R 194 ASN R 216 HIS R 281 GLN R 345 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.185788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137552 restraints weight = 10834.798| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.36 r_work: 0.3450 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2176 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= 0.149 Angle : 0.550 6.105 12239 Z= 0.296 Chirality : 0.043 0.145 1406 Planarity : 0.004 0.042 1547 Dihedral : 4.549 53.013 1236 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.31 % Allowed : 11.03 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.25), residues: 1129 helix: 2.06 (0.26), residues: 397 sheet: 0.74 (0.29), residues: 299 loop : 0.21 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 32 TYR 0.018 0.001 TYR E 190 PHE 0.015 0.001 PHE B 151 TRP 0.018 0.002 TRP R 248 HIS 0.003 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9010) covalent geometry : angle 0.54951 (12233) SS BOND : bond 0.00303 ( 3) SS BOND : angle 0.96535 ( 6) hydrogen bonds : bond 0.05188 ( 461) hydrogen bonds : angle 5.12149 ( 1311) *********************** 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 228 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.8980 (m) cc_final: 0.8673 (p) REVERT: A 290 TYR cc_start: 0.8576 (t80) cc_final: 0.8316 (t80) REVERT: A 314 LYS cc_start: 0.7819 (mttt) cc_final: 0.7398 (mtpt) REVERT: B 19 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7603 (ttp80) REVERT: B 23 LYS cc_start: 0.7790 (ttmm) cc_final: 0.7463 (mmmt) REVERT: B 170 ASP cc_start: 0.8572 (t70) cc_final: 0.8242 (t0) REVERT: B 186 ASP cc_start: 0.8737 (m-30) cc_final: 0.8360 (m-30) REVERT: B 188 MET cc_start: 0.8692 (mmm) cc_final: 0.7990 (mmp) REVERT: B 214 ARG cc_start: 0.8296 (mmt180) cc_final: 0.7951 (mmt180) REVERT: B 277 SER cc_start: 0.8079 (t) cc_final: 0.7803 (m) REVERT: B 303 ASP cc_start: 0.7593 (m-30) cc_final: 0.7296 (m-30) REVERT: C 15 LEU cc_start: 0.9165 (mm) cc_final: 0.8848 (tt) REVERT: C 17 GLU cc_start: 0.8957 (tp30) cc_final: 0.8689 (tp30) REVERT: C 32 LYS cc_start: 0.8208 (tppt) cc_final: 0.7879 (tttt) REVERT: C 38 MET cc_start: 0.7138 (ttp) cc_final: 0.6462 (tpt) REVERT: E 46 GLU cc_start: 0.8215 (tt0) cc_final: 0.7596 (tt0) REVERT: E 83 MET cc_start: 0.8213 (mtm) cc_final: 0.8009 (mtm) REVERT: E 94 TYR cc_start: 0.8646 (m-80) cc_final: 0.8404 (m-80) REVERT: E 160 ARG cc_start: 0.7705 (mtp-110) cc_final: 0.6937 (ttm-80) REVERT: E 175 TYR cc_start: 0.8476 (m-80) cc_final: 0.8122 (m-80) REVERT: E 186 GLN cc_start: 0.8447 (tt0) cc_final: 0.8062 (tt0) REVERT: E 224 VAL cc_start: 0.7438 (t) cc_final: 0.7235 (p) REVERT: R 165 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7714 (ptp) REVERT: R 342 TYR cc_start: 0.7916 (m-80) cc_final: 0.7530 (m-80) REVERT: R 380 TYR cc_start: 0.7945 (t80) cc_final: 0.7739 (t80) REVERT: R 388 ARG cc_start: 0.7744 (ttp-170) cc_final: 0.7235 (ttp-110) outliers start: 22 outliers final: 12 residues processed: 218 average time/residue: 0.1198 time to fit residues: 34.1328 Evaluate side-chains 193 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 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 165 MET Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 249 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 69 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 39 optimal weight: 0.0070 chunk 55 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.189371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137829 restraints weight = 10794.095| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.40 r_work: 0.3481 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 9013 Z= 0.112 Angle : 0.499 6.735 12239 Z= 0.264 Chirality : 0.042 0.149 1406 Planarity : 0.003 0.042 1547 Dihedral : 3.942 25.589 1232 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.10 % Allowed : 13.03 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.25), residues: 1129 helix: 2.31 (0.26), residues: 395 sheet: 0.69 (0.29), residues: 288 loop : 0.20 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 322 TYR 0.038 0.002 TYR R 360 PHE 0.033 0.001 PHE R 387 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9010) covalent geometry : angle 0.49842 (12233) SS BOND : bond 0.00255 ( 3) SS BOND : angle 0.70852 ( 6) hydrogen bonds : bond 0.04170 ( 461) hydrogen bonds : angle 4.71121 ( 1311) *********************** 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 201 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.8799 (m) cc_final: 0.8542 (p) REVERT: A 290 TYR cc_start: 0.8586 (t80) cc_final: 0.8278 (t80) REVERT: A 314 LYS cc_start: 0.7815 (mttt) cc_final: 0.7504 (mtpt) REVERT: B 13 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8220 (pp30) REVERT: B 19 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7791 (ttp80) REVERT: B 36 ASN cc_start: 0.8586 (m-40) cc_final: 0.8274 (p0) REVERT: B 170 ASP cc_start: 0.8547 (t70) cc_final: 0.8286 (t0) REVERT: B 186 ASP cc_start: 0.8697 (m-30) cc_final: 0.8419 (m-30) REVERT: B 214 ARG cc_start: 0.8297 (mmt180) cc_final: 0.7948 (mmt180) REVERT: B 277 SER cc_start: 0.8001 (t) cc_final: 0.7745 (m) REVERT: B 303 ASP cc_start: 0.7539 (m-30) cc_final: 0.7211 (m-30) REVERT: C 17 GLU cc_start: 0.8977 (tp30) cc_final: 0.8668 (tp30) REVERT: C 38 MET cc_start: 0.6993 (ttp) cc_final: 0.6350 (tpt) REVERT: E 46 GLU cc_start: 0.8090 (tt0) cc_final: 0.7521 (tt0) REVERT: E 140 MET cc_start: 0.7566 (mmm) cc_final: 0.7148 (mmm) REVERT: E 142 GLN cc_start: 0.6768 (mt0) cc_final: 0.6247 (mt0) REVERT: E 160 ARG cc_start: 0.7752 (mtp-110) cc_final: 0.6923 (ttm-80) REVERT: E 186 GLN cc_start: 0.8429 (tt0) cc_final: 0.7997 (pt0) REVERT: E 224 VAL cc_start: 0.7435 (t) cc_final: 0.7224 (p) REVERT: R 165 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7444 (ptp) REVERT: R 278 THR cc_start: 0.8667 (m) cc_final: 0.8447 (t) REVERT: R 303 ARG cc_start: 0.7271 (mtp85) cc_final: 0.7040 (mtm180) REVERT: R 325 ARG cc_start: 0.8411 (ptp90) cc_final: 0.7966 (ttp80) REVERT: R 342 TYR cc_start: 0.8194 (m-80) cc_final: 0.7777 (m-80) REVERT: R 370 TYR cc_start: 0.6804 (m-10) cc_final: 0.6402 (m-10) REVERT: R 388 ARG cc_start: 0.7687 (ttp-170) cc_final: 0.7255 (ttp-110) outliers start: 20 outliers final: 11 residues processed: 190 average time/residue: 0.1224 time to fit residues: 30.2991 Evaluate side-chains 186 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 17 GLN Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 343 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 0.0170 chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 0.0870 chunk 36 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.186123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134189 restraints weight = 11037.565| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.42 r_work: 0.3435 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9013 Z= 0.148 Angle : 0.520 5.744 12239 Z= 0.275 Chirality : 0.042 0.143 1406 Planarity : 0.003 0.041 1547 Dihedral : 3.960 25.199 1232 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.10 % Allowed : 13.87 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.25), residues: 1129 helix: 2.32 (0.26), residues: 396 sheet: 0.48 (0.29), residues: 303 loop : 0.12 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 322 TYR 0.035 0.002 TYR R 360 PHE 0.033 0.001 PHE R 387 TRP 0.011 0.001 TRP B 99 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9010) covalent geometry : angle 0.51992 (12233) SS BOND : bond 0.00298 ( 3) SS BOND : angle 0.76979 ( 6) hydrogen bonds : bond 0.04089 ( 461) hydrogen bonds : angle 4.64302 ( 1311) *********************** 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 192 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.8798 (m) cc_final: 0.8548 (p) REVERT: A 290 TYR cc_start: 0.8630 (t80) cc_final: 0.8211 (t80) REVERT: A 314 LYS cc_start: 0.7843 (mttt) cc_final: 0.7529 (mtpt) REVERT: B 13 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8228 (pp30) REVERT: B 19 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7872 (ttp80) REVERT: B 36 ASN cc_start: 0.8625 (m-40) cc_final: 0.8353 (p0) REVERT: B 170 ASP cc_start: 0.8611 (t70) cc_final: 0.8364 (t0) REVERT: B 186 ASP cc_start: 0.8828 (m-30) cc_final: 0.8511 (m-30) REVERT: B 217 MET cc_start: 0.7977 (ptm) cc_final: 0.7486 (ptm) REVERT: B 277 SER cc_start: 0.8151 (t) cc_final: 0.7877 (m) REVERT: B 303 ASP cc_start: 0.7620 (m-30) cc_final: 0.7295 (m-30) REVERT: C 38 MET cc_start: 0.6951 (ttp) cc_final: 0.6326 (tpt) REVERT: E 46 GLU cc_start: 0.8154 (tt0) cc_final: 0.7622 (tt0) REVERT: E 142 GLN cc_start: 0.6823 (mt0) cc_final: 0.6247 (mt0) REVERT: E 160 ARG cc_start: 0.7940 (mtp-110) cc_final: 0.7182 (ttm-80) REVERT: E 224 VAL cc_start: 0.7499 (t) cc_final: 0.7286 (p) REVERT: E 234 GLU cc_start: 0.8457 (tp30) cc_final: 0.8209 (tp30) REVERT: R 165 MET cc_start: 0.7995 (ttp) cc_final: 0.7230 (ptp) REVERT: R 303 ARG cc_start: 0.7374 (mtp85) cc_final: 0.7164 (mtp85) REVERT: R 325 ARG cc_start: 0.8432 (ptp90) cc_final: 0.7957 (ttp80) REVERT: R 342 TYR cc_start: 0.8476 (m-80) cc_final: 0.7972 (m-80) REVERT: R 370 TYR cc_start: 0.7037 (m-80) cc_final: 0.6620 (m-80) REVERT: R 380 TYR cc_start: 0.8390 (t80) cc_final: 0.7971 (t80) outliers start: 20 outliers final: 17 residues processed: 181 average time/residue: 0.1283 time to fit residues: 30.0826 Evaluate side-chains 182 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 313 ARG Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 217 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.183558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.131074 restraints weight = 10925.124| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.43 r_work: 0.3395 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9013 Z= 0.202 Angle : 0.554 6.460 12239 Z= 0.296 Chirality : 0.044 0.150 1406 Planarity : 0.004 0.040 1547 Dihedral : 4.158 27.412 1232 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.15 % Allowed : 13.34 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.25), residues: 1129 helix: 2.27 (0.26), residues: 396 sheet: 0.19 (0.28), residues: 316 loop : 0.16 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 134 TYR 0.037 0.002 TYR R 360 PHE 0.030 0.002 PHE R 387 TRP 0.014 0.002 TRP B 99 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 9010) covalent geometry : angle 0.55415 (12233) SS BOND : bond 0.00313 ( 3) SS BOND : angle 0.87192 ( 6) hydrogen bonds : bond 0.04276 ( 461) hydrogen bonds : angle 4.74255 ( 1311) *********************** 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 208 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8112 (ttm) cc_final: 0.7905 (ttm) REVERT: A 197 LYS cc_start: 0.8381 (mtmt) cc_final: 0.7915 (mtmt) REVERT: A 252 SER cc_start: 0.9017 (m) cc_final: 0.8736 (p) REVERT: A 290 TYR cc_start: 0.8618 (t80) cc_final: 0.8259 (t80) REVERT: A 314 LYS cc_start: 0.7916 (mttt) cc_final: 0.7573 (mtpt) REVERT: B 19 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7872 (ttp80) REVERT: B 36 ASN cc_start: 0.8600 (m-40) cc_final: 0.8334 (p0) REVERT: B 170 ASP cc_start: 0.8607 (t70) cc_final: 0.8351 (t0) REVERT: B 186 ASP cc_start: 0.8879 (m-30) cc_final: 0.8581 (m-30) REVERT: B 277 SER cc_start: 0.8226 (t) cc_final: 0.7944 (m) REVERT: B 303 ASP cc_start: 0.7768 (m-30) cc_final: 0.7437 (m-30) REVERT: C 38 MET cc_start: 0.7085 (ttp) cc_final: 0.6445 (tpt) REVERT: E 46 GLU cc_start: 0.8182 (tt0) cc_final: 0.7643 (tt0) REVERT: E 142 GLN cc_start: 0.6881 (mt0) cc_final: 0.6173 (mt0) REVERT: E 160 ARG cc_start: 0.7945 (mtp-110) cc_final: 0.7263 (ttm-80) REVERT: E 224 VAL cc_start: 0.7476 (t) cc_final: 0.7253 (p) REVERT: E 234 GLU cc_start: 0.8474 (tp30) cc_final: 0.8051 (tp30) REVERT: R 280 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.6860 (t80) REVERT: R 325 ARG cc_start: 0.8385 (ptp90) cc_final: 0.7902 (ttp80) REVERT: R 342 TYR cc_start: 0.8535 (m-80) cc_final: 0.8004 (m-80) REVERT: R 380 TYR cc_start: 0.8494 (t80) cc_final: 0.8050 (t80) outliers start: 30 outliers final: 23 residues processed: 189 average time/residue: 0.1257 time to fit residues: 30.8928 Evaluate side-chains 190 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 136 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 85 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 7 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.185480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136433 restraints weight = 10924.507| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.73 r_work: 0.3416 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9013 Z= 0.130 Angle : 0.511 5.542 12239 Z= 0.272 Chirality : 0.042 0.136 1406 Planarity : 0.003 0.039 1547 Dihedral : 4.057 28.114 1232 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.52 % Allowed : 13.87 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.25), residues: 1129 helix: 2.40 (0.26), residues: 396 sheet: 0.26 (0.29), residues: 308 loop : 0.17 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.039 0.001 TYR R 360 PHE 0.034 0.001 PHE R 387 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9010) covalent geometry : angle 0.50891 (12233) SS BOND : bond 0.00141 ( 3) SS BOND : angle 2.06755 ( 6) hydrogen bonds : bond 0.03801 ( 461) hydrogen bonds : angle 4.59472 ( 1311) *********************** 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 198 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7687 (ttm) cc_final: 0.7475 (ttm) REVERT: A 252 SER cc_start: 0.8968 (m) cc_final: 0.8702 (p) REVERT: A 290 TYR cc_start: 0.8659 (t80) cc_final: 0.8276 (t80) REVERT: A 314 LYS cc_start: 0.7873 (mttt) cc_final: 0.7553 (mtpt) REVERT: B 19 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7843 (ttp80) REVERT: B 170 ASP cc_start: 0.8410 (t70) cc_final: 0.8199 (t0) REVERT: B 186 ASP cc_start: 0.8708 (m-30) cc_final: 0.8460 (m-30) REVERT: B 217 MET cc_start: 0.7945 (ptm) cc_final: 0.7281 (ptm) REVERT: B 264 TYR cc_start: 0.7948 (m-80) cc_final: 0.7097 (m-80) REVERT: B 277 SER cc_start: 0.7982 (t) cc_final: 0.7734 (m) REVERT: B 303 ASP cc_start: 0.7616 (m-30) cc_final: 0.7203 (m-30) REVERT: C 38 MET cc_start: 0.6658 (ttp) cc_final: 0.6147 (tpt) REVERT: E 46 GLU cc_start: 0.8036 (tt0) cc_final: 0.7476 (tt0) REVERT: E 160 ARG cc_start: 0.7901 (mtp-110) cc_final: 0.7227 (ttm-80) REVERT: E 175 TYR cc_start: 0.8445 (m-80) cc_final: 0.8147 (m-80) REVERT: E 186 GLN cc_start: 0.8157 (tt0) cc_final: 0.7881 (pt0) REVERT: E 224 VAL cc_start: 0.7492 (t) cc_final: 0.7269 (p) REVERT: E 234 GLU cc_start: 0.8309 (tp30) cc_final: 0.7929 (tp30) REVERT: R 165 MET cc_start: 0.7895 (ttp) cc_final: 0.7000 (ptp) REVERT: R 249 LEU cc_start: 0.8247 (mm) cc_final: 0.7885 (tt) REVERT: R 280 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.6490 (t80) REVERT: R 342 TYR cc_start: 0.8457 (m-80) cc_final: 0.8020 (m-80) REVERT: R 388 ARG cc_start: 0.7574 (ttp-170) cc_final: 0.7188 (ttp-110) outliers start: 24 outliers final: 20 residues processed: 183 average time/residue: 0.1224 time to fit residues: 29.2200 Evaluate side-chains 189 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 85 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 0.4980 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.189234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148004 restraints weight = 10538.935| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.22 r_work: 0.3519 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9013 Z= 0.117 Angle : 0.493 5.511 12239 Z= 0.263 Chirality : 0.041 0.135 1406 Planarity : 0.003 0.039 1547 Dihedral : 3.961 28.369 1232 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.63 % Allowed : 14.60 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.26), residues: 1129 helix: 2.35 (0.26), residues: 401 sheet: 0.38 (0.30), residues: 295 loop : 0.17 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.040 0.002 TYR R 360 PHE 0.033 0.001 PHE R 387 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9010) covalent geometry : angle 0.49261 (12233) SS BOND : bond 0.00141 ( 3) SS BOND : angle 1.15803 ( 6) hydrogen bonds : bond 0.03600 ( 461) hydrogen bonds : angle 4.48078 ( 1311) *********************** 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 202 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7963 (mttt) REVERT: A 252 SER cc_start: 0.8965 (m) cc_final: 0.8752 (p) REVERT: A 290 TYR cc_start: 0.8670 (t80) cc_final: 0.8261 (t80) REVERT: A 314 LYS cc_start: 0.8037 (mttt) cc_final: 0.7738 (mtpt) REVERT: B 19 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7976 (ttp80) REVERT: B 186 ASP cc_start: 0.8774 (m-30) cc_final: 0.8519 (m-30) REVERT: B 217 MET cc_start: 0.8113 (ptm) cc_final: 0.7466 (ptm) REVERT: B 264 TYR cc_start: 0.8021 (m-80) cc_final: 0.7221 (m-80) REVERT: B 277 SER cc_start: 0.8015 (t) cc_final: 0.7806 (m) REVERT: B 303 ASP cc_start: 0.7886 (m-30) cc_final: 0.7472 (m-30) REVERT: C 28 ILE cc_start: 0.8891 (pt) cc_final: 0.8684 (tp) REVERT: C 38 MET cc_start: 0.6924 (ttp) cc_final: 0.6360 (tpt) REVERT: E 46 GLU cc_start: 0.8037 (tt0) cc_final: 0.7569 (tt0) REVERT: E 103 TYR cc_start: 0.8460 (t80) cc_final: 0.8187 (t80) REVERT: E 160 ARG cc_start: 0.7959 (mtp-110) cc_final: 0.7349 (ttm-80) REVERT: E 175 TYR cc_start: 0.8443 (m-80) cc_final: 0.8219 (m-80) REVERT: E 186 GLN cc_start: 0.8289 (tt0) cc_final: 0.8086 (pt0) REVERT: E 224 VAL cc_start: 0.7405 (t) cc_final: 0.7195 (p) REVERT: E 234 GLU cc_start: 0.8413 (tp30) cc_final: 0.8035 (tp30) REVERT: R 165 MET cc_start: 0.7952 (ttp) cc_final: 0.7141 (ptp) REVERT: R 249 LEU cc_start: 0.8247 (mm) cc_final: 0.7992 (tt) REVERT: R 280 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.6539 (t80) REVERT: R 342 TYR cc_start: 0.8468 (m-80) cc_final: 0.8046 (m-80) REVERT: R 370 TYR cc_start: 0.7119 (m-80) cc_final: 0.6474 (m-80) REVERT: R 380 TYR cc_start: 0.8417 (t80) cc_final: 0.8040 (t80) REVERT: R 388 ARG cc_start: 0.7542 (ttp-170) cc_final: 0.7156 (ttp-110) outliers start: 25 outliers final: 21 residues processed: 191 average time/residue: 0.1171 time to fit residues: 29.2172 Evaluate side-chains 193 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 197 LYS 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 C residue 42 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 116 THR 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 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.192233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140688 restraints weight = 10714.964| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.37 r_work: 0.3524 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9013 Z= 0.115 Angle : 0.502 5.642 12239 Z= 0.266 Chirality : 0.041 0.136 1406 Planarity : 0.003 0.038 1547 Dihedral : 3.949 27.898 1232 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.52 % Allowed : 14.81 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.26), residues: 1129 helix: 2.41 (0.26), residues: 401 sheet: 0.37 (0.30), residues: 295 loop : 0.16 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 303 TYR 0.042 0.002 TYR R 360 PHE 0.036 0.001 PHE R 387 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9010) covalent geometry : angle 0.50189 (12233) SS BOND : bond 0.00129 ( 3) SS BOND : angle 1.08937 ( 6) hydrogen bonds : bond 0.03511 ( 461) hydrogen bonds : angle 4.44474 ( 1311) *********************** 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: 24 poor density : 171 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8497 (ttpp) cc_final: 0.7929 (tptp) REVERT: A 252 SER cc_start: 0.8816 (m) cc_final: 0.8569 (p) REVERT: A 290 TYR cc_start: 0.8663 (t80) cc_final: 0.8255 (t80) REVERT: A 314 LYS cc_start: 0.7918 (mttt) cc_final: 0.7623 (mtpt) REVERT: B 19 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7955 (ttp80) REVERT: B 175 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8000 (pt0) REVERT: B 186 ASP cc_start: 0.8777 (m-30) cc_final: 0.8513 (m-30) REVERT: B 264 TYR cc_start: 0.8013 (m-80) cc_final: 0.7271 (m-80) REVERT: B 277 SER cc_start: 0.8048 (t) cc_final: 0.7821 (m) REVERT: B 303 ASP cc_start: 0.7877 (m-30) cc_final: 0.7484 (m-30) REVERT: C 28 ILE cc_start: 0.8907 (pt) cc_final: 0.8696 (tp) REVERT: C 38 MET cc_start: 0.6780 (ttp) cc_final: 0.6216 (tpt) REVERT: E 46 GLU cc_start: 0.8017 (tt0) cc_final: 0.7536 (tt0) REVERT: E 83 MET cc_start: 0.8033 (mtm) cc_final: 0.7805 (mtm) REVERT: E 103 TYR cc_start: 0.8440 (t80) cc_final: 0.8209 (t80) REVERT: E 160 ARG cc_start: 0.7962 (mtp-110) cc_final: 0.7214 (ttm-80) REVERT: E 175 TYR cc_start: 0.8539 (m-80) cc_final: 0.8287 (m-80) REVERT: E 186 GLN cc_start: 0.8308 (tt0) cc_final: 0.8092 (pt0) REVERT: E 218 ARG cc_start: 0.6820 (ttp-170) cc_final: 0.6605 (ttp-170) REVERT: E 224 VAL cc_start: 0.7344 (t) cc_final: 0.7119 (p) REVERT: E 234 GLU cc_start: 0.8420 (tp30) cc_final: 0.8014 (tp30) REVERT: R 249 LEU cc_start: 0.8244 (mm) cc_final: 0.8043 (tt) REVERT: R 280 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6551 (t80) REVERT: R 342 TYR cc_start: 0.8473 (m-80) cc_final: 0.8073 (m-80) REVERT: R 380 TYR cc_start: 0.8386 (t80) cc_final: 0.8070 (t80) REVERT: R 388 ARG cc_start: 0.7568 (ttp-170) cc_final: 0.7196 (ttp-110) outliers start: 24 outliers final: 20 residues processed: 183 average time/residue: 0.1168 time to fit residues: 28.2856 Evaluate side-chains 190 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 C residue 42 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 116 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 23 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 9 optimal weight: 0.0670 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.192281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140965 restraints weight = 10700.079| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.37 r_work: 0.3532 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3400 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= 0.113 Angle : 0.514 6.071 12239 Z= 0.270 Chirality : 0.042 0.141 1406 Planarity : 0.004 0.038 1547 Dihedral : 3.929 27.254 1232 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.63 % Allowed : 14.92 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.25), residues: 1129 helix: 2.45 (0.26), residues: 399 sheet: 0.44 (0.31), residues: 280 loop : 0.12 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 46 TYR 0.043 0.002 TYR R 360 PHE 0.035 0.001 PHE R 387 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9010) covalent geometry : angle 0.51402 (12233) SS BOND : bond 0.00137 ( 3) SS BOND : angle 0.98616 ( 6) hydrogen bonds : bond 0.03467 ( 461) hydrogen bonds : angle 4.41720 ( 1311) *********************** 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 203 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8498 (ttpp) cc_final: 0.7933 (tptp) REVERT: A 197 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7418 (mttt) REVERT: A 252 SER cc_start: 0.8817 (m) cc_final: 0.8555 (p) REVERT: A 290 TYR cc_start: 0.8658 (t80) cc_final: 0.8306 (t80) REVERT: A 312 LYS cc_start: 0.7806 (tppt) cc_final: 0.7517 (mmtp) REVERT: A 314 LYS cc_start: 0.7939 (mttt) cc_final: 0.7644 (mtpt) REVERT: B 19 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7910 (ttp80) REVERT: B 175 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8003 (pt0) REVERT: B 186 ASP cc_start: 0.8777 (m-30) cc_final: 0.8495 (m-30) REVERT: B 217 MET cc_start: 0.7961 (ptm) cc_final: 0.7179 (ptm) REVERT: B 264 TYR cc_start: 0.8000 (m-80) cc_final: 0.7278 (m-80) REVERT: B 277 SER cc_start: 0.8040 (t) cc_final: 0.7817 (m) REVERT: B 303 ASP cc_start: 0.7825 (m-30) cc_final: 0.7409 (m-30) REVERT: C 28 ILE cc_start: 0.8906 (pt) cc_final: 0.8698 (tp) REVERT: C 38 MET cc_start: 0.6739 (ttp) cc_final: 0.6191 (tpt) REVERT: E 46 GLU cc_start: 0.7996 (tt0) cc_final: 0.7527 (tt0) REVERT: E 103 TYR cc_start: 0.8444 (t80) cc_final: 0.8205 (t80) REVERT: E 160 ARG cc_start: 0.7915 (mtp-110) cc_final: 0.7178 (ttm-80) REVERT: E 175 TYR cc_start: 0.8552 (m-80) cc_final: 0.8307 (m-80) REVERT: E 186 GLN cc_start: 0.8297 (tt0) cc_final: 0.8081 (pt0) REVERT: E 218 ARG cc_start: 0.6830 (ttp-170) cc_final: 0.6610 (ttp-170) REVERT: E 224 VAL cc_start: 0.7331 (t) cc_final: 0.7123 (p) REVERT: R 180 PHE cc_start: 0.7811 (m-10) cc_final: 0.7608 (t80) REVERT: R 280 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6492 (t80) REVERT: R 325 ARG cc_start: 0.8386 (ptp90) cc_final: 0.7896 (ttp80) REVERT: R 342 TYR cc_start: 0.8472 (m-80) cc_final: 0.8068 (m-80) REVERT: R 380 TYR cc_start: 0.8348 (t80) cc_final: 0.8071 (t80) REVERT: R 388 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.7152 (ttp-110) outliers start: 25 outliers final: 20 residues processed: 189 average time/residue: 0.1248 time to fit residues: 30.7182 Evaluate side-chains 196 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 197 LYS 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 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 116 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN E 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.189388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.145346 restraints weight = 10701.422| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.50 r_work: 0.3502 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3450 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= 0.135 Angle : 0.537 8.574 12239 Z= 0.281 Chirality : 0.042 0.149 1406 Planarity : 0.004 0.041 1547 Dihedral : 3.996 27.614 1232 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.42 % Allowed : 15.44 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.26), residues: 1129 helix: 2.47 (0.26), residues: 399 sheet: 0.37 (0.30), residues: 293 loop : 0.09 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 46 TYR 0.043 0.002 TYR R 360 PHE 0.035 0.001 PHE R 387 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9010) covalent geometry : angle 0.53695 (12233) SS BOND : bond 0.00111 ( 3) SS BOND : angle 0.99841 ( 6) hydrogen bonds : bond 0.03569 ( 461) hydrogen bonds : angle 4.43571 ( 1311) ********************** 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 199 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7335 (mttt) REVERT: A 252 SER cc_start: 0.8976 (m) cc_final: 0.8752 (p) REVERT: A 314 LYS cc_start: 0.7980 (mttt) cc_final: 0.7695 (mtpt) REVERT: B 13 GLN cc_start: 0.8372 (pp30) cc_final: 0.8058 (pp30) REVERT: B 19 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7918 (ttp80) REVERT: B 175 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8058 (pt0) REVERT: B 186 ASP cc_start: 0.8667 (m-30) cc_final: 0.8442 (m-30) REVERT: B 217 MET cc_start: 0.7840 (ptm) cc_final: 0.7125 (ptm) REVERT: B 264 TYR cc_start: 0.7988 (m-80) cc_final: 0.7244 (m-80) REVERT: B 303 ASP cc_start: 0.7760 (m-30) cc_final: 0.7330 (m-30) REVERT: C 38 MET cc_start: 0.6630 (ttp) cc_final: 0.6178 (tpt) REVERT: E 46 GLU cc_start: 0.7894 (tt0) cc_final: 0.7452 (tt0) REVERT: E 83 MET cc_start: 0.7925 (mtm) cc_final: 0.7684 (mtm) REVERT: E 103 TYR cc_start: 0.8375 (t80) cc_final: 0.8100 (t80) REVERT: E 160 ARG cc_start: 0.7845 (mtp-110) cc_final: 0.7243 (ttm-80) REVERT: E 175 TYR cc_start: 0.8446 (m-80) cc_final: 0.8244 (m-80) REVERT: E 186 GLN cc_start: 0.8174 (tt0) cc_final: 0.7964 (pt0) REVERT: E 218 ARG cc_start: 0.6767 (ttp-170) cc_final: 0.6563 (ttp-170) REVERT: E 224 VAL cc_start: 0.7364 (t) cc_final: 0.7163 (p) REVERT: E 234 GLU cc_start: 0.8254 (tp30) cc_final: 0.7841 (tp30) REVERT: R 280 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6637 (t80) REVERT: R 325 ARG cc_start: 0.8388 (ptp90) cc_final: 0.7873 (ttp80) REVERT: R 342 TYR cc_start: 0.8357 (m-80) cc_final: 0.8024 (m-80) REVERT: R 380 TYR cc_start: 0.8238 (t80) cc_final: 0.7971 (t80) REVERT: R 388 ARG cc_start: 0.7511 (ttp-170) cc_final: 0.7161 (ttp-110) outliers start: 23 outliers final: 19 residues processed: 184 average time/residue: 0.1206 time to fit residues: 28.9553 Evaluate side-chains 195 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 197 LYS 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 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 116 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 0.0040 chunk 41 optimal weight: 0.0980 chunk 80 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 84 optimal weight: 0.0570 chunk 49 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.3710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN E 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.189434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.148298 restraints weight = 10517.402| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.38 r_work: 0.3551 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9013 Z= 0.100 Angle : 0.515 8.499 12239 Z= 0.270 Chirality : 0.041 0.137 1406 Planarity : 0.004 0.039 1547 Dihedral : 3.912 26.938 1232 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.00 % Allowed : 16.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.26), residues: 1129 helix: 2.41 (0.26), residues: 401 sheet: 0.44 (0.31), residues: 280 loop : 0.13 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 46 TYR 0.044 0.002 TYR R 360 PHE 0.034 0.001 PHE R 387 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9010) covalent geometry : angle 0.51511 (12233) SS BOND : bond 0.00163 ( 3) SS BOND : angle 0.83441 ( 6) hydrogen bonds : bond 0.03281 ( 461) hydrogen bonds : angle 4.34538 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2933.88 seconds wall clock time: 50 minutes 56.46 seconds (3056.46 seconds total)