Starting phenix.real_space_refine on Sun Jul 27 20:34:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f16_31405/07_2025/7f16_31405_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f16_31405/07_2025/7f16_31405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f16_31405/07_2025/7f16_31405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f16_31405/07_2025/7f16_31405.map" model { file = "/net/cci-nas-00/data/ceres_data/7f16_31405/07_2025/7f16_31405_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f16_31405/07_2025/7f16_31405_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 58 5.16 5 C 6106 2.51 5 N 1619 2.21 5 O 1705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9488 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3072 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 10, 'TRANS': 365} Chain breaks: 3 Chain: "P" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 282 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1905 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" 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: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 220 Unusual residues: {'CLR': 4, 'PLM': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 5.55, per 1000 atoms: 0.58 Number of scatterers: 9488 At special positions: 0 Unit cell: (74.195, 101.365, 172.425, 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 58 16.00 O 1705 8.00 N 1619 7.00 C 6106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 72 " distance=2.03 Simple disulfide: pdb=" SG CYS R 63 " - pdb=" SG CYS R 103 " distance=2.03 Simple disulfide: pdb=" SG CYS R 86 " - pdb=" SG CYS R 125 " distance=2.04 Simple disulfide: pdb=" SG CYS R 236 " - pdb=" SG CYS R 306 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.0 seconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 44.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'R' and resid 33 through 57 removed outlier: 3.882A pdb=" N THR R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA R 54 " --> pdb=" O LEU R 50 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN R 55 " --> pdb=" O ASN R 51 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN R 57 " --> pdb=" O THR R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 169 removed outlier: 3.871A pdb=" N ASP R 132 " --> pdb=" O PHE R 128 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU R 159 " --> pdb=" O SER R 155 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL R 161 " --> pdb=" O GLY R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.561A pdb=" N ILE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 267 removed outlier: 4.167A pdb=" N LYS R 237 " --> pdb=" O TYR R 233 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA R 248 " --> pdb=" O ILE R 244 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN R 263 " --> pdb=" O LEU R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 302 Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 315 through 347 Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 354 through 373 Processing helix chain 'R' and resid 373 through 381 removed outlier: 4.172A pdb=" N ILE R 377 " --> pdb=" O GLY R 373 " (cutoff:3.500A) Processing helix chain 'R' and resid 389 through 414 removed outlier: 4.489A pdb=" N GLY R 406 " --> pdb=" O ASN R 402 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE R 407 " --> pdb=" O SER R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 417 through 434 Processing helix chain 'P' and resid 4 through 34 Processing helix chain 'A' and resid 12 through 40 removed outlier: 4.265A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.512A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.949A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.776A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.396A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.545A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.613A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.556A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.936A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 81 through 85 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.609A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 7.063A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.868A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.294A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.497A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.696A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.657A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.543A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.996A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3030 1.34 - 1.47: 2348 1.47 - 1.59: 4242 1.59 - 1.71: 0 1.71 - 1.83: 80 Bond restraints: 9700 Sorted by residual: bond pdb=" C PHE R 286 " pdb=" N PRO R 287 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.58e+00 bond pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.32e-02 5.74e+03 3.30e+00 bond pdb=" C5 CLR R 503 " pdb=" C6 CLR R 503 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C ALA R 320 " pdb=" N PRO R 321 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.39e+00 bond pdb=" C5 CLR R 502 " pdb=" C6 CLR R 502 " ideal model delta sigma weight residual 1.332 1.302 0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 9695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 12467 1.77 - 3.54: 544 3.54 - 5.31: 81 5.31 - 7.07: 22 7.07 - 8.84: 3 Bond angle restraints: 13117 Sorted by residual: angle pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " pdb=" CG TYR R 148 " ideal model delta sigma weight residual 113.90 121.73 -7.83 1.80e+00 3.09e-01 1.89e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 124.31 130.25 -5.94 1.67e+00 3.59e-01 1.27e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 122.74 127.49 -4.75 1.44e+00 4.82e-01 1.09e+01 angle pdb=" N GLY B 116 " pdb=" CA GLY B 116 " pdb=" C GLY B 116 " ideal model delta sigma weight residual 111.27 116.50 -5.23 1.67e+00 3.59e-01 9.82e+00 angle pdb=" C MET R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.14 115.67 5.47 1.75e+00 3.27e-01 9.78e+00 ... (remaining 13112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 5777 18.02 - 36.04: 127 36.04 - 54.05: 35 54.05 - 72.07: 3 72.07 - 90.09: 3 Dihedral angle restraints: 5945 sinusoidal: 2570 harmonic: 3375 Sorted by residual: dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 72 " pdb=" CB CYS R 72 " ideal model delta sinusoidal sigma weight residual -86.00 -176.09 90.09 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CA TYR R 233 " pdb=" C TYR R 233 " pdb=" N ILE R 234 " pdb=" CA ILE R 234 " ideal model delta harmonic sigma weight residual -180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ARG A 231 " pdb=" C ARG A 231 " pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 5942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1295 0.090 - 0.180: 131 0.180 - 0.270: 9 0.270 - 0.360: 4 0.360 - 0.451: 4 Chirality restraints: 1443 Sorted by residual: chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.77 0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" C14 CLR R 501 " pdb=" C13 CLR R 501 " pdb=" C15 CLR R 501 " pdb=" C8 CLR R 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.77 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" C14 CLR R 503 " pdb=" C13 CLR R 503 " pdb=" C15 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 1440 not shown) Planarity restraints: 1639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 242 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C MET R 242 " -0.049 2.00e-02 2.50e+03 pdb=" O MET R 242 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE R 243 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.46e+00 pdb=" N PRO A 332 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.043 5.00e-02 4.00e+02 6.57e-02 6.92e+00 pdb=" N PRO A 361 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.036 5.00e-02 4.00e+02 ... (remaining 1636 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1343 2.77 - 3.30: 8742 3.30 - 3.84: 15530 3.84 - 4.37: 17916 4.37 - 4.90: 31547 Nonbonded interactions: 75078 Sorted by model distance: nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.240 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.301 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.307 3.040 ... (remaining 75073 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: 0.590 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.370 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:14.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.004 0.049 9706 Z= 0.212 Angle : 0.848 8.843 13129 Z= 0.471 Chirality : 0.060 0.451 1443 Planarity : 0.006 0.068 1639 Dihedral : 8.872 77.994 3747 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1141 helix: 1.29 (0.20), residues: 464 sheet: 0.82 (0.36), residues: 211 loop : -0.84 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 281 HIS 0.022 0.003 HIS A 220 PHE 0.032 0.003 PHE R 290 TYR 0.024 0.002 TYR R 178 ARG 0.006 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.10641 ( 496) hydrogen bonds : angle 5.73090 ( 1425) SS BOND : bond 0.00241 ( 6) SS BOND : angle 2.58627 ( 12) covalent geometry : bond 0.00379 ( 9700) covalent geometry : angle 0.84436 (13117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 33 THR cc_start: 0.8198 (m) cc_final: 0.6786 (m) REVERT: R 70 LEU cc_start: 0.8501 (tp) cc_final: 0.8227 (pt) REVERT: R 86 CYS cc_start: 0.3613 (m) cc_final: 0.3144 (m) REVERT: R 371 VAL cc_start: 0.8306 (t) cc_final: 0.7947 (p) REVERT: R 410 SER cc_start: 0.8490 (t) cc_final: 0.8211 (p) REVERT: A 221 MET cc_start: 0.7304 (ttp) cc_final: 0.7027 (ttp) REVERT: A 344 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7065 (tp30) REVERT: B 280 LYS cc_start: 0.8534 (tttp) cc_final: 0.8268 (tttp) REVERT: N 11 LEU cc_start: 0.8565 (tp) cc_final: 0.8222 (tm) REVERT: N 73 ASP cc_start: 0.7387 (t0) cc_final: 0.6774 (t0) REVERT: N 78 THR cc_start: 0.6547 (m) cc_final: 0.6237 (m) REVERT: N 95 TYR cc_start: 0.8595 (m-10) cc_final: 0.8372 (m-80) outliers start: 0 outliers final: 1 residues processed: 340 average time/residue: 1.1424 time to fit residues: 415.9612 Evaluate side-chains 204 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 GLN R 204 HIS R 250 ASN R 396 HIS A 59 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS B 91 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.151960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115189 restraints weight = 14977.072| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.97 r_work: 0.3427 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9706 Z= 0.151 Angle : 0.591 7.649 13129 Z= 0.316 Chirality : 0.043 0.280 1443 Planarity : 0.005 0.059 1639 Dihedral : 6.770 57.583 1615 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.13 % Allowed : 16.89 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.24), residues: 1141 helix: 2.29 (0.22), residues: 466 sheet: 0.68 (0.34), residues: 230 loop : -0.34 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 281 HIS 0.007 0.001 HIS B 225 PHE 0.032 0.002 PHE R 290 TYR 0.027 0.002 TYR R 148 ARG 0.007 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 496) hydrogen bonds : angle 4.50637 ( 1425) SS BOND : bond 0.00397 ( 6) SS BOND : angle 1.81417 ( 12) covalent geometry : bond 0.00335 ( 9700) covalent geometry : angle 0.58915 (13117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8536 (mp0) cc_final: 0.7962 (pm20) REVERT: R 93 PHE cc_start: 0.8910 (m-80) cc_final: 0.8646 (m-80) REVERT: R 281 LEU cc_start: 0.8194 (tm) cc_final: 0.7961 (tm) REVERT: R 416 CYS cc_start: 0.8266 (t) cc_final: 0.7974 (m) REVERT: P 16 LEU cc_start: 0.8000 (tm) cc_final: 0.7752 (tm) REVERT: P 20 LEU cc_start: 0.9011 (mt) cc_final: 0.8735 (mt) REVERT: A 33 ASP cc_start: 0.8267 (t70) cc_final: 0.7803 (m-30) REVERT: A 35 GLN cc_start: 0.7977 (mt0) cc_final: 0.7506 (mm-40) REVERT: A 283 ARG cc_start: 0.7657 (mtm180) cc_final: 0.7436 (mtp-110) REVERT: A 336 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7067 (tpt-90) REVERT: B 155 ASN cc_start: 0.7757 (t0) cc_final: 0.7053 (t0) REVERT: B 172 GLU cc_start: 0.8537 (mm-30) cc_final: 0.7900 (mm-30) REVERT: B 230 ASN cc_start: 0.8745 (m-40) cc_final: 0.8212 (m-40) REVERT: B 280 LYS cc_start: 0.8766 (tttp) cc_final: 0.8374 (tttp) REVERT: B 303 ASP cc_start: 0.7142 (p0) cc_final: 0.6924 (p0) REVERT: G 21 MET cc_start: 0.6319 (tmm) cc_final: 0.5892 (tmm) REVERT: N 11 LEU cc_start: 0.8343 (tp) cc_final: 0.8115 (tm) REVERT: N 73 ASP cc_start: 0.7513 (t0) cc_final: 0.6664 (t0) REVERT: N 82 GLN cc_start: 0.7818 (tp-100) cc_final: 0.7375 (tp40) REVERT: N 95 TYR cc_start: 0.8459 (m-10) cc_final: 0.7989 (m-80) outliers start: 31 outliers final: 11 residues processed: 240 average time/residue: 1.1296 time to fit residues: 291.0621 Evaluate side-chains 188 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 96 optimal weight: 0.0470 chunk 17 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 GLN ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN R 396 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.147255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108025 restraints weight = 15404.112| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.94 r_work: 0.3361 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9706 Z= 0.136 Angle : 0.554 6.546 13129 Z= 0.295 Chirality : 0.041 0.274 1443 Planarity : 0.004 0.040 1639 Dihedral : 6.447 58.161 1613 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.04 % Allowed : 18.60 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1141 helix: 2.47 (0.23), residues: 465 sheet: 0.56 (0.34), residues: 228 loop : -0.29 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 281 HIS 0.004 0.001 HIS A 357 PHE 0.028 0.002 PHE R 290 TYR 0.026 0.002 TYR P 29 ARG 0.008 0.001 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 496) hydrogen bonds : angle 4.35526 ( 1425) SS BOND : bond 0.00508 ( 6) SS BOND : angle 0.98885 ( 12) covalent geometry : bond 0.00309 ( 9700) covalent geometry : angle 0.55301 (13117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: R 33 THR cc_start: 0.8272 (m) cc_final: 0.7876 (m) REVERT: R 35 GLU cc_start: 0.8560 (mp0) cc_final: 0.8129 (pm20) REVERT: R 93 PHE cc_start: 0.8813 (m-80) cc_final: 0.8598 (m-80) REVERT: R 281 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8019 (tm) REVERT: R 309 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7469 (mm) REVERT: R 357 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7449 (pp30) REVERT: R 416 CYS cc_start: 0.8223 (t) cc_final: 0.7931 (m) REVERT: R 431 TRP cc_start: 0.7814 (t60) cc_final: 0.7561 (t60) REVERT: P 12 GLU cc_start: 0.8192 (tp30) cc_final: 0.7976 (tp30) REVERT: P 16 LEU cc_start: 0.7972 (tm) cc_final: 0.7647 (tm) REVERT: P 20 LEU cc_start: 0.8920 (mt) cc_final: 0.8556 (mt) REVERT: A 14 ASN cc_start: 0.9151 (m110) cc_final: 0.8804 (p0) REVERT: A 33 ASP cc_start: 0.8217 (t70) cc_final: 0.7769 (m-30) REVERT: A 35 GLN cc_start: 0.7991 (mt0) cc_final: 0.7478 (mm-40) REVERT: A 283 ARG cc_start: 0.7812 (mtm180) cc_final: 0.7294 (mtp-110) REVERT: A 333 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8472 (pmm-80) REVERT: A 336 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7060 (tpt-90) REVERT: A 356 ARG cc_start: 0.6567 (ptp-170) cc_final: 0.6351 (pmm-80) REVERT: B 145 TYR cc_start: 0.8825 (p90) cc_final: 0.8540 (p90) REVERT: B 155 ASN cc_start: 0.7677 (t0) cc_final: 0.6893 (t0) REVERT: B 172 GLU cc_start: 0.8639 (mm-30) cc_final: 0.7982 (mm-30) REVERT: B 230 ASN cc_start: 0.8598 (m-40) cc_final: 0.8327 (m110) REVERT: B 259 GLN cc_start: 0.8162 (pt0) cc_final: 0.7752 (pm20) REVERT: B 267 ASP cc_start: 0.8900 (m-30) cc_final: 0.8680 (m-30) REVERT: B 273 ILE cc_start: 0.8998 (mp) cc_final: 0.8661 (mp) REVERT: B 280 LYS cc_start: 0.8774 (tttp) cc_final: 0.8498 (tttp) REVERT: G 21 MET cc_start: 0.6578 (tmm) cc_final: 0.6189 (tmm) REVERT: N 11 LEU cc_start: 0.8368 (tp) cc_final: 0.8119 (tm) REVERT: N 34 MET cc_start: 0.8130 (mtp) cc_final: 0.7439 (mtp) REVERT: N 73 ASP cc_start: 0.7549 (t0) cc_final: 0.6788 (t0) REVERT: N 76 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8492 (ttmm) REVERT: N 82 GLN cc_start: 0.7759 (tp-100) cc_final: 0.7278 (tp40) REVERT: N 89 GLU cc_start: 0.8927 (pp20) cc_final: 0.8464 (tm-30) REVERT: N 95 TYR cc_start: 0.8346 (m-10) cc_final: 0.8128 (m-80) REVERT: N 105 ARG cc_start: 0.8274 (mtm180) cc_final: 0.7424 (mtp85) outliers start: 40 outliers final: 10 residues processed: 210 average time/residue: 1.1749 time to fit residues: 264.0875 Evaluate side-chains 190 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 357 GLN Chi-restraints excluded: chain R residue 393 ILE Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 303 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 0.0770 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 75 optimal weight: 0.0770 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 396 HIS ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.150181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.111981 restraints weight = 15050.480| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.96 r_work: 0.3347 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9706 Z= 0.118 Angle : 0.531 8.645 13129 Z= 0.281 Chirality : 0.040 0.226 1443 Planarity : 0.004 0.040 1639 Dihedral : 6.188 58.772 1613 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.83 % Allowed : 20.22 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1141 helix: 2.47 (0.23), residues: 470 sheet: 0.36 (0.34), residues: 228 loop : -0.27 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 253 HIS 0.005 0.001 HIS R 180 PHE 0.026 0.001 PHE R 290 TYR 0.024 0.002 TYR R 148 ARG 0.009 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 496) hydrogen bonds : angle 4.23529 ( 1425) SS BOND : bond 0.00236 ( 6) SS BOND : angle 1.03246 ( 12) covalent geometry : bond 0.00263 ( 9700) covalent geometry : angle 0.53082 (13117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8552 (mp0) cc_final: 0.8330 (mp0) REVERT: R 93 PHE cc_start: 0.8880 (m-80) cc_final: 0.8672 (m-80) REVERT: R 273 THR cc_start: 0.7803 (m) cc_final: 0.7557 (t) REVERT: R 281 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8301 (tm) REVERT: R 309 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7686 (mm) REVERT: R 416 CYS cc_start: 0.8260 (t) cc_final: 0.8040 (m) REVERT: P 12 GLU cc_start: 0.8439 (tp30) cc_final: 0.8190 (tp30) REVERT: P 20 LEU cc_start: 0.8966 (mt) cc_final: 0.8570 (mt) REVERT: P 31 HIS cc_start: 0.8492 (p-80) cc_final: 0.8240 (p90) REVERT: A 14 ASN cc_start: 0.9088 (m110) cc_final: 0.8787 (p0) REVERT: A 33 ASP cc_start: 0.8282 (t70) cc_final: 0.7970 (m-30) REVERT: A 35 GLN cc_start: 0.8144 (mt0) cc_final: 0.7701 (mm-40) REVERT: A 38 ARG cc_start: 0.9055 (mmm-85) cc_final: 0.8849 (mmt90) REVERT: A 220 HIS cc_start: 0.7389 (m170) cc_final: 0.6944 (m170) REVERT: A 283 ARG cc_start: 0.8012 (mtm180) cc_final: 0.7624 (mtp-110) REVERT: A 336 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7539 (tpt-90) REVERT: A 344 GLU cc_start: 0.7406 (tt0) cc_final: 0.7163 (mt-10) REVERT: B 155 ASN cc_start: 0.7909 (t0) cc_final: 0.7453 (t0) REVERT: B 172 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8257 (mm-30) REVERT: B 273 ILE cc_start: 0.9028 (mp) cc_final: 0.8746 (mp) REVERT: B 280 LYS cc_start: 0.8894 (tttp) cc_final: 0.8603 (tttp) REVERT: G 21 MET cc_start: 0.6747 (tmm) cc_final: 0.6367 (tmm) REVERT: N 11 LEU cc_start: 0.8497 (tp) cc_final: 0.8246 (tm) REVERT: N 34 MET cc_start: 0.7984 (mtp) cc_final: 0.7615 (mtp) REVERT: N 73 ASP cc_start: 0.7763 (t0) cc_final: 0.7015 (t0) REVERT: N 76 LYS cc_start: 0.8752 (ttmm) cc_final: 0.8452 (ttmm) REVERT: N 80 TYR cc_start: 0.7176 (m-80) cc_final: 0.6886 (m-80) REVERT: N 82 GLN cc_start: 0.8184 (tp-100) cc_final: 0.7609 (tp40) REVERT: N 89 GLU cc_start: 0.8869 (pp20) cc_final: 0.8372 (tm-30) outliers start: 28 outliers final: 9 residues processed: 205 average time/residue: 1.1328 time to fit residues: 249.0682 Evaluate side-chains 183 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 319 GLN R 396 HIS ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.143854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.103434 restraints weight = 14826.719| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.90 r_work: 0.3188 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9706 Z= 0.205 Angle : 0.584 6.831 13129 Z= 0.314 Chirality : 0.043 0.225 1443 Planarity : 0.004 0.054 1639 Dihedral : 6.258 58.369 1613 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.55 % Allowed : 18.71 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1141 helix: 2.58 (0.23), residues: 455 sheet: 0.03 (0.33), residues: 235 loop : -0.23 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 431 HIS 0.006 0.001 HIS A 357 PHE 0.021 0.002 PHE R 290 TYR 0.028 0.002 TYR P 29 ARG 0.011 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 496) hydrogen bonds : angle 4.40118 ( 1425) SS BOND : bond 0.01013 ( 6) SS BOND : angle 1.71296 ( 12) covalent geometry : bond 0.00471 ( 9700) covalent geometry : angle 0.58170 (13117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 1.087 Fit side-chains REVERT: R 35 GLU cc_start: 0.8651 (mp0) cc_final: 0.8166 (mp0) REVERT: R 93 PHE cc_start: 0.8979 (m-80) cc_final: 0.8726 (m-80) REVERT: R 309 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7797 (mm) REVERT: R 319 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7921 (tp40) REVERT: R 357 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7623 (pp30) REVERT: R 416 CYS cc_start: 0.8440 (t) cc_final: 0.8232 (m) REVERT: P 16 LEU cc_start: 0.8246 (tm) cc_final: 0.7942 (tm) REVERT: P 20 LEU cc_start: 0.8989 (mt) cc_final: 0.8575 (mt) REVERT: P 31 HIS cc_start: 0.8585 (p-80) cc_final: 0.8306 (p90) REVERT: A 14 ASN cc_start: 0.9103 (m110) cc_final: 0.8806 (OUTLIER) REVERT: A 33 ASP cc_start: 0.8350 (t70) cc_final: 0.8112 (m-30) REVERT: A 35 GLN cc_start: 0.8279 (mt0) cc_final: 0.7839 (mm-40) REVERT: A 336 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7446 (tpt-90) REVERT: A 365 CYS cc_start: 0.8349 (m) cc_final: 0.7454 (t) REVERT: B 155 ASN cc_start: 0.8101 (t0) cc_final: 0.7611 (t0) REVERT: B 172 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8404 (mm-30) REVERT: B 217 MET cc_start: 0.8809 (pmm) cc_final: 0.8559 (pmm) REVERT: B 226 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8153 (mt-10) REVERT: B 259 GLN cc_start: 0.8674 (pt0) cc_final: 0.8423 (pt0) REVERT: G 21 MET cc_start: 0.6780 (tmm) cc_final: 0.6342 (tmm) REVERT: G 38 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.6869 (mtm) REVERT: N 34 MET cc_start: 0.8331 (mtp) cc_final: 0.8128 (mtp) REVERT: N 46 GLU cc_start: 0.8809 (pt0) cc_final: 0.8541 (pt0) REVERT: N 73 ASP cc_start: 0.7878 (t0) cc_final: 0.7229 (t0) REVERT: N 76 LYS cc_start: 0.8939 (ttmm) cc_final: 0.8654 (ttmm) REVERT: N 85 SER cc_start: 0.9077 (m) cc_final: 0.8745 (p) REVERT: N 89 GLU cc_start: 0.8947 (pp20) cc_final: 0.8318 (tm-30) REVERT: N 105 ARG cc_start: 0.8461 (mtm180) cc_final: 0.7732 (mtp85) outliers start: 45 outliers final: 19 residues processed: 208 average time/residue: 1.2019 time to fit residues: 268.0181 Evaluate side-chains 186 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 319 GLN Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 357 GLN Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 50.0000 chunk 71 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 88 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: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 HIS R 319 GLN R 375 HIS R 396 HIS B 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.144900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.104981 restraints weight = 14836.056| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.90 r_work: 0.3211 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9706 Z= 0.142 Angle : 0.554 8.493 13129 Z= 0.294 Chirality : 0.041 0.177 1443 Planarity : 0.004 0.057 1639 Dihedral : 6.160 59.270 1613 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.64 % Allowed : 22.04 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1141 helix: 2.66 (0.23), residues: 457 sheet: -0.10 (0.33), residues: 228 loop : -0.23 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 119 HIS 0.005 0.001 HIS A 357 PHE 0.032 0.002 PHE B 292 TYR 0.026 0.002 TYR P 29 ARG 0.012 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 496) hydrogen bonds : angle 4.36248 ( 1425) SS BOND : bond 0.00266 ( 6) SS BOND : angle 1.45906 ( 12) covalent geometry : bond 0.00325 ( 9700) covalent geometry : angle 0.55227 (13117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8668 (mp0) cc_final: 0.8462 (mp0) REVERT: R 93 PHE cc_start: 0.8978 (m-80) cc_final: 0.8767 (m-80) REVERT: R 273 THR cc_start: 0.8447 (p) cc_final: 0.7945 (t) REVERT: R 309 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7768 (mm) REVERT: R 319 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7997 (tp40) REVERT: R 357 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7654 (pp30) REVERT: R 431 TRP cc_start: 0.7885 (t-100) cc_final: 0.7389 (t60) REVERT: P 16 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7950 (tm) REVERT: P 20 LEU cc_start: 0.9014 (mt) cc_final: 0.8609 (mt) REVERT: P 31 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.8289 (p90) REVERT: A 14 ASN cc_start: 0.9113 (m110) cc_final: 0.8807 (OUTLIER) REVERT: A 33 ASP cc_start: 0.8264 (t70) cc_final: 0.8036 (m-30) REVERT: A 35 GLN cc_start: 0.8295 (mt0) cc_final: 0.7865 (mm-40) REVERT: A 292 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8558 (m110) REVERT: A 336 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7405 (tpt-90) REVERT: A 365 CYS cc_start: 0.8468 (m) cc_final: 0.7550 (t) REVERT: A 390 GLN cc_start: 0.8960 (mt0) cc_final: 0.8732 (mt0) REVERT: B 155 ASN cc_start: 0.8099 (t0) cc_final: 0.7475 (t0) REVERT: B 172 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8349 (mm-30) REVERT: B 226 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8233 (mt-10) REVERT: B 259 GLN cc_start: 0.8642 (pt0) cc_final: 0.8394 (pt0) REVERT: B 264 TYR cc_start: 0.9007 (m-80) cc_final: 0.8683 (m-80) REVERT: B 292 PHE cc_start: 0.8599 (m-80) cc_final: 0.8021 (m-80) REVERT: G 21 MET cc_start: 0.6662 (tmm) cc_final: 0.6214 (tmm) REVERT: G 38 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6848 (mtm) REVERT: N 34 MET cc_start: 0.8199 (mtp) cc_final: 0.7946 (mtp) REVERT: N 46 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8522 (pt0) REVERT: N 73 ASP cc_start: 0.7905 (t0) cc_final: 0.7223 (t0) REVERT: N 76 LYS cc_start: 0.8972 (ttmm) cc_final: 0.8696 (ttmm) REVERT: N 80 TYR cc_start: 0.7714 (m-80) cc_final: 0.7450 (m-80) REVERT: N 85 SER cc_start: 0.9070 (m) cc_final: 0.8737 (p) REVERT: N 89 GLU cc_start: 0.8987 (pp20) cc_final: 0.8293 (tm-30) REVERT: N 105 ARG cc_start: 0.8451 (mtm180) cc_final: 0.7746 (mtp85) outliers start: 36 outliers final: 15 residues processed: 193 average time/residue: 1.2296 time to fit residues: 254.2367 Evaluate side-chains 180 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 319 GLN Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 357 GLN Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 31 HIS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 0.0870 chunk 106 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 30.0000 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN R 396 HIS B 44 GLN B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.144651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.104557 restraints weight = 14954.079| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.91 r_work: 0.3207 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9706 Z= 0.143 Angle : 0.558 7.379 13129 Z= 0.298 Chirality : 0.041 0.159 1443 Planarity : 0.004 0.059 1639 Dihedral : 5.984 58.554 1613 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.34 % Allowed : 22.95 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1141 helix: 2.56 (0.23), residues: 462 sheet: -0.13 (0.32), residues: 230 loop : -0.31 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 119 HIS 0.006 0.001 HIS A 220 PHE 0.022 0.001 PHE R 290 TYR 0.027 0.002 TYR P 29 ARG 0.012 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 496) hydrogen bonds : angle 4.34179 ( 1425) SS BOND : bond 0.00232 ( 6) SS BOND : angle 1.40333 ( 12) covalent geometry : bond 0.00327 ( 9700) covalent geometry : angle 0.55636 (13117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 1.000 Fit side-chains REVERT: R 169 PHE cc_start: 0.6842 (m-10) cc_final: 0.6505 (m-80) REVERT: R 233 TYR cc_start: 0.7539 (m-80) cc_final: 0.7257 (m-10) REVERT: R 273 THR cc_start: 0.8445 (p) cc_final: 0.7956 (t) REVERT: R 309 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7701 (mm) REVERT: R 319 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8065 (tp40) REVERT: R 431 TRP cc_start: 0.7908 (t-100) cc_final: 0.7424 (t60) REVERT: P 16 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7956 (tm) REVERT: P 20 LEU cc_start: 0.9019 (mt) cc_final: 0.8614 (mt) REVERT: P 21 GLU cc_start: 0.8633 (pp20) cc_final: 0.8278 (pp20) REVERT: P 31 HIS cc_start: 0.8601 (OUTLIER) cc_final: 0.8280 (p90) REVERT: A 14 ASN cc_start: 0.9112 (m110) cc_final: 0.8809 (OUTLIER) REVERT: A 27 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8388 (tp30) REVERT: A 35 GLN cc_start: 0.8274 (mt0) cc_final: 0.7842 (mm-40) REVERT: A 336 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7412 (tpt-90) REVERT: A 344 GLU cc_start: 0.7735 (tt0) cc_final: 0.7478 (mt-10) REVERT: A 365 CYS cc_start: 0.8491 (m) cc_final: 0.8272 (m) REVERT: A 372 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8411 (mp) REVERT: A 390 GLN cc_start: 0.8950 (mt0) cc_final: 0.8714 (mt0) REVERT: B 155 ASN cc_start: 0.8130 (t0) cc_final: 0.7462 (t0) REVERT: B 172 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8349 (mm-30) REVERT: B 259 GLN cc_start: 0.8580 (pt0) cc_final: 0.8355 (pt0) REVERT: B 264 TYR cc_start: 0.8993 (m-80) cc_final: 0.8663 (m-80) REVERT: B 267 ASP cc_start: 0.8820 (m-30) cc_final: 0.8587 (m-30) REVERT: B 292 PHE cc_start: 0.8557 (m-80) cc_final: 0.8021 (m-80) REVERT: B 312 ASP cc_start: 0.8757 (p0) cc_final: 0.8413 (p0) REVERT: G 21 MET cc_start: 0.6732 (tmm) cc_final: 0.6314 (tmm) REVERT: G 38 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.7025 (mtm) REVERT: N 34 MET cc_start: 0.8220 (mtp) cc_final: 0.7988 (mtp) REVERT: N 46 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8485 (pt0) REVERT: N 73 ASP cc_start: 0.7919 (t0) cc_final: 0.7206 (t0) REVERT: N 76 LYS cc_start: 0.8992 (ttmm) cc_final: 0.8697 (ttmm) REVERT: N 80 TYR cc_start: 0.7748 (m-80) cc_final: 0.7472 (m-80) REVERT: N 85 SER cc_start: 0.9088 (m) cc_final: 0.8761 (p) REVERT: N 105 ARG cc_start: 0.8447 (mtm180) cc_final: 0.7724 (mtp85) outliers start: 33 outliers final: 17 residues processed: 189 average time/residue: 1.1398 time to fit residues: 231.5261 Evaluate side-chains 177 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 319 GLN Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 31 HIS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 85 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN R 396 HIS B 44 GLN B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.142029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.101888 restraints weight = 15115.281| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.91 r_work: 0.3190 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9706 Z= 0.160 Angle : 0.581 8.275 13129 Z= 0.309 Chirality : 0.041 0.148 1443 Planarity : 0.004 0.060 1639 Dihedral : 5.955 57.746 1613 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.83 % Allowed : 23.36 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1141 helix: 2.53 (0.23), residues: 462 sheet: -0.15 (0.33), residues: 223 loop : -0.33 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 119 HIS 0.006 0.001 HIS A 220 PHE 0.021 0.002 PHE R 290 TYR 0.030 0.002 TYR N 95 ARG 0.008 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 496) hydrogen bonds : angle 4.37124 ( 1425) SS BOND : bond 0.00212 ( 6) SS BOND : angle 1.50296 ( 12) covalent geometry : bond 0.00370 ( 9700) covalent geometry : angle 0.57926 (13117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8560 (mp0) cc_final: 0.8119 (pm20) REVERT: R 273 THR cc_start: 0.8490 (p) cc_final: 0.8007 (t) REVERT: R 431 TRP cc_start: 0.7889 (t-100) cc_final: 0.7403 (t60) REVERT: P 16 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8011 (tm) REVERT: P 20 LEU cc_start: 0.9031 (mt) cc_final: 0.8634 (mt) REVERT: P 21 GLU cc_start: 0.8613 (pp20) cc_final: 0.8259 (pp20) REVERT: P 31 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8265 (p90) REVERT: A 14 ASN cc_start: 0.9093 (m110) cc_final: 0.8788 (OUTLIER) REVERT: A 27 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8404 (tp30) REVERT: A 35 GLN cc_start: 0.8271 (mt0) cc_final: 0.7864 (mm-40) REVERT: A 336 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7416 (tpt-90) REVERT: A 344 GLU cc_start: 0.7779 (tt0) cc_final: 0.7531 (mt-10) REVERT: A 365 CYS cc_start: 0.8469 (m) cc_final: 0.8225 (m) REVERT: A 372 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 390 GLN cc_start: 0.8978 (mt0) cc_final: 0.8721 (mt0) REVERT: B 155 ASN cc_start: 0.8160 (t0) cc_final: 0.7483 (t0) REVERT: B 172 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8367 (mm-30) REVERT: B 264 TYR cc_start: 0.9060 (m-80) cc_final: 0.8720 (m-80) REVERT: B 292 PHE cc_start: 0.8603 (m-80) cc_final: 0.8092 (m-80) REVERT: B 312 ASP cc_start: 0.8720 (p0) cc_final: 0.8488 (p0) REVERT: G 21 MET cc_start: 0.6781 (tmm) cc_final: 0.6356 (tmm) REVERT: N 34 MET cc_start: 0.8216 (mtp) cc_final: 0.7995 (mtp) REVERT: N 46 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8525 (pt0) REVERT: N 73 ASP cc_start: 0.7901 (t0) cc_final: 0.7245 (t0) REVERT: N 76 LYS cc_start: 0.9021 (ttmm) cc_final: 0.8741 (ttmm) REVERT: N 85 SER cc_start: 0.9131 (m) cc_final: 0.8800 (p) REVERT: N 105 ARG cc_start: 0.8434 (mtm180) cc_final: 0.7725 (mtp85) outliers start: 28 outliers final: 16 residues processed: 182 average time/residue: 1.1811 time to fit residues: 230.4029 Evaluate side-chains 173 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 31 HIS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 0.0050 chunk 90 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN R 396 HIS B 44 GLN B 230 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.144732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105120 restraints weight = 14877.998| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.86 r_work: 0.3185 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9706 Z= 0.133 Angle : 0.576 7.961 13129 Z= 0.307 Chirality : 0.041 0.138 1443 Planarity : 0.004 0.061 1639 Dihedral : 5.867 57.740 1613 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.53 % Allowed : 23.66 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1141 helix: 2.60 (0.23), residues: 462 sheet: -0.22 (0.33), residues: 224 loop : -0.29 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 119 HIS 0.005 0.001 HIS A 220 PHE 0.023 0.001 PHE R 290 TYR 0.028 0.002 TYR R 168 ARG 0.008 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 496) hydrogen bonds : angle 4.36320 ( 1425) SS BOND : bond 0.00224 ( 6) SS BOND : angle 1.64113 ( 12) covalent geometry : bond 0.00304 ( 9700) covalent geometry : angle 0.57399 (13117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8529 (mp0) cc_final: 0.8275 (mp0) REVERT: R 233 TYR cc_start: 0.7646 (m-80) cc_final: 0.7333 (m-10) REVERT: R 273 THR cc_start: 0.8506 (p) cc_final: 0.8016 (t) REVERT: R 431 TRP cc_start: 0.7921 (t-100) cc_final: 0.7388 (t60) REVERT: P 16 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7843 (tm) REVERT: P 20 LEU cc_start: 0.8988 (mt) cc_final: 0.8609 (mt) REVERT: P 21 GLU cc_start: 0.8521 (pp20) cc_final: 0.8179 (pp20) REVERT: P 31 HIS cc_start: 0.8635 (OUTLIER) cc_final: 0.8309 (p90) REVERT: A 14 ASN cc_start: 0.9146 (m110) cc_final: 0.8828 (p0) REVERT: A 27 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8331 (tp30) REVERT: A 35 GLN cc_start: 0.8257 (mt0) cc_final: 0.7775 (mm-40) REVERT: A 336 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7268 (tpt-90) REVERT: A 344 GLU cc_start: 0.7741 (tt0) cc_final: 0.7484 (mt-10) REVERT: A 365 CYS cc_start: 0.8410 (m) cc_final: 0.8183 (m) REVERT: A 378 ASP cc_start: 0.8511 (m-30) cc_final: 0.8285 (m-30) REVERT: A 390 GLN cc_start: 0.8943 (mt0) cc_final: 0.8687 (mt0) REVERT: B 155 ASN cc_start: 0.8058 (t0) cc_final: 0.7351 (t0) REVERT: B 172 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8348 (mm-30) REVERT: B 226 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8110 (mt-10) REVERT: B 264 TYR cc_start: 0.9023 (m-80) cc_final: 0.8645 (m-80) REVERT: B 267 ASP cc_start: 0.8834 (m-30) cc_final: 0.8587 (m-30) REVERT: B 292 PHE cc_start: 0.8555 (m-80) cc_final: 0.7963 (m-80) REVERT: B 312 ASP cc_start: 0.8729 (p0) cc_final: 0.8399 (p0) REVERT: G 21 MET cc_start: 0.6749 (tmm) cc_final: 0.6302 (tmm) REVERT: N 28 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8090 (p) REVERT: N 34 MET cc_start: 0.8190 (mtp) cc_final: 0.7911 (mtp) REVERT: N 46 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8440 (pt0) REVERT: N 73 ASP cc_start: 0.7841 (t0) cc_final: 0.7167 (t0) REVERT: N 76 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8752 (ttmm) REVERT: N 83 MET cc_start: 0.8928 (mtm) cc_final: 0.8641 (ptp) REVERT: N 85 SER cc_start: 0.9151 (m) cc_final: 0.8801 (p) REVERT: N 105 ARG cc_start: 0.8453 (mtm180) cc_final: 0.7686 (mtp85) outliers start: 25 outliers final: 14 residues processed: 177 average time/residue: 1.1852 time to fit residues: 224.5371 Evaluate side-chains 170 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 31 HIS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 30.0000 chunk 83 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN R 396 HIS ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 230 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.144694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105220 restraints weight = 15179.379| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.88 r_work: 0.3186 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9706 Z= 0.134 Angle : 0.618 10.923 13129 Z= 0.325 Chirality : 0.041 0.151 1443 Planarity : 0.004 0.061 1639 Dihedral : 5.902 57.326 1613 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.02 % Allowed : 24.57 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1141 helix: 2.67 (0.23), residues: 462 sheet: -0.30 (0.33), residues: 216 loop : -0.34 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 119 HIS 0.006 0.001 HIS A 220 PHE 0.023 0.002 PHE R 290 TYR 0.027 0.002 TYR P 29 ARG 0.009 0.001 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 496) hydrogen bonds : angle 4.32064 ( 1425) SS BOND : bond 0.00321 ( 6) SS BOND : angle 3.04571 ( 12) covalent geometry : bond 0.00311 ( 9700) covalent geometry : angle 0.61150 (13117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8472 (mp0) cc_final: 0.8208 (mp0) REVERT: R 70 LEU cc_start: 0.8426 (pt) cc_final: 0.8119 (tm) REVERT: R 273 THR cc_start: 0.8508 (p) cc_final: 0.8018 (t) REVERT: R 431 TRP cc_start: 0.7891 (t-100) cc_final: 0.7378 (t60) REVERT: P 16 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7800 (tm) REVERT: P 20 LEU cc_start: 0.8942 (mt) cc_final: 0.8574 (mt) REVERT: P 21 GLU cc_start: 0.8483 (pp20) cc_final: 0.8148 (pp20) REVERT: P 31 HIS cc_start: 0.8681 (OUTLIER) cc_final: 0.8362 (p90) REVERT: A 14 ASN cc_start: 0.9140 (m110) cc_final: 0.8828 (p0) REVERT: A 27 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8332 (tp30) REVERT: A 35 GLN cc_start: 0.8271 (mt0) cc_final: 0.7780 (mm-40) REVERT: A 336 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7295 (tpt-90) REVERT: A 344 GLU cc_start: 0.7709 (tt0) cc_final: 0.7457 (mt-10) REVERT: A 365 CYS cc_start: 0.8407 (m) cc_final: 0.8177 (m) REVERT: A 378 ASP cc_start: 0.8515 (m-30) cc_final: 0.8283 (m-30) REVERT: A 390 GLN cc_start: 0.8936 (mt0) cc_final: 0.8667 (mt0) REVERT: B 155 ASN cc_start: 0.8070 (t0) cc_final: 0.7363 (t0) REVERT: B 172 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8337 (mm-30) REVERT: B 226 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8052 (mt-10) REVERT: B 264 TYR cc_start: 0.9034 (m-80) cc_final: 0.8668 (m-80) REVERT: B 267 ASP cc_start: 0.8858 (m-30) cc_final: 0.8618 (m-30) REVERT: B 301 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8395 (mmmm) REVERT: G 21 MET cc_start: 0.6743 (tmm) cc_final: 0.6300 (tmm) REVERT: N 28 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8042 (p) REVERT: N 34 MET cc_start: 0.8086 (mtp) cc_final: 0.7769 (mtp) REVERT: N 46 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8375 (pt0) REVERT: N 73 ASP cc_start: 0.7868 (t0) cc_final: 0.7180 (t0) REVERT: N 76 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8739 (ttmm) REVERT: N 83 MET cc_start: 0.8917 (mtm) cc_final: 0.8640 (ptp) REVERT: N 85 SER cc_start: 0.9165 (m) cc_final: 0.8795 (p) outliers start: 20 outliers final: 12 residues processed: 175 average time/residue: 1.4328 time to fit residues: 268.4920 Evaluate side-chains 168 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 31 HIS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 29 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN ** R 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 396 HIS B 44 GLN B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.142683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.102488 restraints weight = 14885.541| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.87 r_work: 0.3136 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9706 Z= 0.178 Angle : 0.642 10.474 13129 Z= 0.338 Chirality : 0.042 0.150 1443 Planarity : 0.004 0.060 1639 Dihedral : 5.982 56.410 1613 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.92 % Allowed : 24.47 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1141 helix: 2.66 (0.23), residues: 457 sheet: -0.33 (0.33), residues: 214 loop : -0.28 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.025 0.002 PHE R 169 TYR 0.030 0.002 TYR R 168 ARG 0.009 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 496) hydrogen bonds : angle 4.37812 ( 1425) SS BOND : bond 0.00285 ( 6) SS BOND : angle 2.95688 ( 12) covalent geometry : bond 0.00415 ( 9700) covalent geometry : angle 0.63593 (13117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7769.94 seconds wall clock time: 134 minutes 15.61 seconds (8055.61 seconds total)