Starting phenix.real_space_refine on Sun Dec 29 16:47:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7evz_31342/12_2024/7evz_31342.cif Found real_map, /net/cci-nas-00/data/ceres_data/7evz_31342/12_2024/7evz_31342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7evz_31342/12_2024/7evz_31342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7evz_31342/12_2024/7evz_31342.map" model { file = "/net/cci-nas-00/data/ceres_data/7evz_31342/12_2024/7evz_31342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7evz_31342/12_2024/7evz_31342.cif" } resolution = 3.07 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= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1983 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5810 2.51 5 N 1521 2.21 5 O 1683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9078 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1838 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2296 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 6, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Unusual residues: {'JER': 1, 'PLM': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 6.02, per 1000 atoms: 0.66 Number of scatterers: 9078 At special positions: 0 Unit cell: (90.63, 123.975, 128.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1683 8.00 N 1521 7.00 C 5810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 282 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " 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: 2.59 Conformation dependent library (CDL) restraints added in 1.0 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 36.0% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.521A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.582A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.591A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 216' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.750A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.939A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 4.060A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.583A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.633A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 24 removed outlier: 4.224A pdb=" N GLN C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 23 through 33 Processing helix chain 'D' and resid 49 through 73 removed outlier: 3.576A pdb=" N THR D 73 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 105 removed outlier: 3.503A pdb=" N TYR D 82 " --> pdb=" O ARG D 78 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 84 " --> pdb=" O MET D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.746A pdb=" N THR D 109 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR D 110 " --> pdb=" O ALA D 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 110' Processing helix chain 'D' and resid 113 through 148 removed outlier: 3.512A pdb=" N GLU D 121 " --> pdb=" O TRP D 117 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 181 removed outlier: 4.248A pdb=" N LEU D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 199 through 236 removed outlier: 3.510A pdb=" N ILE D 203 " --> pdb=" O HIS D 199 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 removed outlier: 3.545A pdb=" N LYS D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR D 257 " --> pdb=" O ALA D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 282 removed outlier: 3.977A pdb=" N VAL D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 314 removed outlier: 3.866A pdb=" N LEU D 297 " --> pdb=" O ALA D 293 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 315 through 325 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.545A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.555A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.544A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.940A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.502A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.959A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.536A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.528A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.599A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.512A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.676A pdb=" N VAL E 12 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.506A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1149 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: 2.49 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2274 1.33 - 1.45: 1913 1.45 - 1.58: 4974 1.58 - 1.70: 3 1.70 - 1.82: 91 Bond restraints: 9255 Sorted by residual: bond pdb=" C31 JER D 401 " pdb=" C32 JER D 401 " ideal model delta sigma weight residual 1.543 1.361 0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" C28 JER D 401 " pdb=" C29 JER D 401 " ideal model delta sigma weight residual 1.532 1.354 0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" C28 JER D 401 " pdb=" C32 JER D 401 " ideal model delta sigma weight residual 1.537 1.651 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C10 JER D 401 " pdb=" C15 JER D 401 " ideal model delta sigma weight residual 1.460 1.374 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C22 JER D 401 " pdb=" O23 JER D 401 " ideal model delta sigma weight residual 1.332 1.410 -0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 9250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 12372 2.34 - 4.68: 105 4.68 - 7.03: 18 7.03 - 9.37: 2 9.37 - 11.71: 3 Bond angle restraints: 12500 Sorted by residual: angle pdb=" N PHE D 237 " pdb=" CA PHE D 237 " pdb=" C PHE D 237 " ideal model delta sigma weight residual 111.36 123.07 -11.71 1.09e+00 8.42e-01 1.15e+02 angle pdb=" N ARG D 238 " pdb=" CA ARG D 238 " pdb=" C ARG D 238 " ideal model delta sigma weight residual 113.16 123.13 -9.97 1.24e+00 6.50e-01 6.46e+01 angle pdb=" N LYS D 239 " pdb=" CA LYS D 239 " pdb=" C LYS D 239 " ideal model delta sigma weight residual 110.23 116.35 -6.12 1.45e+00 4.76e-01 1.78e+01 angle pdb=" N THR D 236 " pdb=" CA THR D 236 " pdb=" C THR D 236 " ideal model delta sigma weight residual 109.54 103.76 5.78 1.37e+00 5.33e-01 1.78e+01 angle pdb=" C26 JER D 401 " pdb=" C28 JER D 401 " pdb=" C29 JER D 401 " ideal model delta sigma weight residual 114.08 102.52 11.56 3.00e+00 1.11e-01 1.48e+01 ... (remaining 12495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5012 17.98 - 35.95: 429 35.95 - 53.93: 65 53.93 - 71.91: 11 71.91 - 89.88: 6 Dihedral angle restraints: 5523 sinusoidal: 2203 harmonic: 3320 Sorted by residual: dihedral pdb=" CB CYS D 184 " pdb=" SG CYS D 184 " pdb=" SG CYS D 191 " pdb=" CB CYS D 191 " ideal model delta sinusoidal sigma weight residual -86.00 -47.75 -38.25 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 65.20 27.80 1 1.00e+01 1.00e-02 1.11e+01 dihedral pdb=" CA ASP A 229 " pdb=" CB ASP A 229 " pdb=" CG ASP A 229 " pdb=" OD1 ASP A 229 " ideal model delta sinusoidal sigma weight residual -30.00 -87.29 57.29 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 5520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1357 0.093 - 0.186: 62 0.186 - 0.280: 4 0.280 - 0.373: 0 0.373 - 0.466: 1 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA PHE D 237 " pdb=" N PHE D 237 " pdb=" C PHE D 237 " pdb=" CB PHE D 237 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA GLU D 249 " pdb=" N GLU D 249 " pdb=" C GLU D 249 " pdb=" CB GLU D 249 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA SER D 251 " pdb=" N SER D 251 " pdb=" C SER D 251 " pdb=" CB SER D 251 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1421 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO E 236 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO C 49 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 239 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C LYS D 239 " -0.026 2.00e-02 2.50e+03 pdb=" O LYS D 239 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN D 240 " 0.009 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 289 2.71 - 3.26: 8624 3.26 - 3.80: 13751 3.80 - 4.35: 16884 4.35 - 4.90: 30032 Nonbonded interactions: 69580 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.160 3.040 nonbonded pdb=" OG SER D 192 " pdb=" O LEU D 195 " model vdw 2.180 3.040 nonbonded pdb=" OD2 ASP A 341 " pdb=" NZ LYS D 239 " model vdw 2.206 3.120 nonbonded pdb=" O THR D 236 " pdb=" OG1 THR D 236 " model vdw 2.218 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.259 3.040 ... (remaining 69575 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: 5.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.920 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 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 0.182 9255 Z= 0.278 Angle : 0.585 11.711 12500 Z= 0.336 Chirality : 0.043 0.466 1424 Planarity : 0.003 0.053 1557 Dihedral : 13.326 89.882 3372 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.30 % Allowed : 5.18 % Favored : 94.52 % 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: -1.99 (0.23), residues: 1126 helix: 0.22 (0.24), residues: 382 sheet: -1.46 (0.29), residues: 277 loop : -2.53 (0.23), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 176 HIS 0.003 0.000 HIS D 199 PHE 0.020 0.001 PHE E 108 TYR 0.014 0.001 TYR E 190 ARG 0.004 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 1.030 Fit side-chains REVERT: A 275 GLU cc_start: 0.8062 (tp30) cc_final: 0.7848 (mm-30) REVERT: B 44 GLN cc_start: 0.7721 (tp40) cc_final: 0.7430 (mt0) REVERT: B 137 ARG cc_start: 0.7464 (tpp-160) cc_final: 0.6979 (tpt90) REVERT: B 197 ARG cc_start: 0.7291 (tpp80) cc_final: 0.7004 (tpp80) REVERT: B 217 MET cc_start: 0.7100 (ptt) cc_final: 0.6529 (ptm) REVERT: B 274 THR cc_start: 0.8559 (m) cc_final: 0.8235 (p) REVERT: B 280 LYS cc_start: 0.8172 (tptp) cc_final: 0.7920 (tptt) REVERT: B 289 TYR cc_start: 0.8866 (m-80) cc_final: 0.7606 (m-80) REVERT: B 292 PHE cc_start: 0.8510 (m-10) cc_final: 0.8252 (m-10) REVERT: B 312 ASP cc_start: 0.8438 (t0) cc_final: 0.8035 (t0) REVERT: D 190 SER cc_start: 0.6529 (m) cc_final: 0.6206 (t) REVERT: D 224 ILE cc_start: 0.6056 (tt) cc_final: 0.5765 (tt) REVERT: D 292 ARG cc_start: 0.8190 (mtt90) cc_final: 0.7508 (mtm180) REVERT: E 93 MET cc_start: 0.6976 (ttm) cc_final: 0.6028 (ttm) REVERT: E 192 MET cc_start: 0.5588 (tpp) cc_final: 0.4274 (ptp) outliers start: 3 outliers final: 2 residues processed: 155 average time/residue: 0.2894 time to fit residues: 57.8813 Evaluate side-chains 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 249 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 6 GLN B 75 GLN D 240 ASN D 303 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9255 Z= 0.279 Angle : 0.572 7.532 12500 Z= 0.295 Chirality : 0.042 0.181 1424 Planarity : 0.004 0.062 1557 Dihedral : 6.101 71.781 1320 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.32 % Allowed : 12.99 % Favored : 85.69 % 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: -0.99 (0.24), residues: 1126 helix: 1.51 (0.26), residues: 381 sheet: -1.19 (0.31), residues: 278 loop : -2.19 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 176 HIS 0.005 0.001 HIS B 62 PHE 0.016 0.002 PHE A 189 TYR 0.020 0.002 TYR E 190 ARG 0.005 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8652 (mtp) cc_final: 0.8394 (mtp) REVERT: A 275 GLU cc_start: 0.8108 (tp30) cc_final: 0.7726 (mm-30) REVERT: B 197 ARG cc_start: 0.7327 (tpp80) cc_final: 0.7067 (tpp80) REVERT: B 217 MET cc_start: 0.7205 (ptt) cc_final: 0.6726 (ptm) REVERT: B 274 THR cc_start: 0.8626 (m) cc_final: 0.8249 (p) REVERT: B 280 LYS cc_start: 0.8247 (tptp) cc_final: 0.8036 (tptt) REVERT: B 292 PHE cc_start: 0.8665 (m-10) cc_final: 0.8349 (m-10) REVERT: B 312 ASP cc_start: 0.8373 (t0) cc_final: 0.7892 (t0) REVERT: E 82 GLN cc_start: 0.7391 (tp-100) cc_final: 0.7090 (tp40) REVERT: E 93 MET cc_start: 0.7109 (ttm) cc_final: 0.6293 (ttm) REVERT: E 140 MET cc_start: 0.8706 (mmm) cc_final: 0.8292 (mmm) outliers start: 13 outliers final: 8 residues processed: 140 average time/residue: 0.2973 time to fit residues: 54.3149 Evaluate side-chains 129 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9255 Z= 0.313 Angle : 0.586 8.582 12500 Z= 0.303 Chirality : 0.043 0.196 1424 Planarity : 0.004 0.067 1557 Dihedral : 6.254 78.509 1316 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.25 % Allowed : 16.04 % Favored : 80.71 % 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: -0.69 (0.25), residues: 1126 helix: 1.92 (0.27), residues: 382 sheet: -1.22 (0.31), residues: 282 loop : -2.04 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.004 0.001 HIS B 62 PHE 0.016 0.002 PHE B 235 TYR 0.028 0.002 TYR E 235 ARG 0.005 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8649 (mtp) cc_final: 0.8362 (mtp) REVERT: A 275 GLU cc_start: 0.8174 (tp30) cc_final: 0.7723 (mm-30) REVERT: B 175 GLN cc_start: 0.7820 (pt0) cc_final: 0.6863 (pm20) REVERT: B 217 MET cc_start: 0.7249 (ptt) cc_final: 0.6778 (ptm) REVERT: B 280 LYS cc_start: 0.8274 (tptp) cc_final: 0.8022 (tptt) REVERT: B 292 PHE cc_start: 0.8710 (m-10) cc_final: 0.8439 (m-10) REVERT: B 312 ASP cc_start: 0.8354 (t0) cc_final: 0.7824 (t0) REVERT: D 190 SER cc_start: 0.6978 (m) cc_final: 0.6378 (t) REVERT: D 227 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6517 (mp) REVERT: E 82 GLN cc_start: 0.7394 (tp-100) cc_final: 0.7056 (tp40) REVERT: E 140 MET cc_start: 0.8699 (mmm) cc_final: 0.8169 (mmm) outliers start: 32 outliers final: 21 residues processed: 154 average time/residue: 0.2545 time to fit residues: 52.5895 Evaluate side-chains 150 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 32 GLN B 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9255 Z= 0.206 Angle : 0.523 7.621 12500 Z= 0.269 Chirality : 0.041 0.172 1424 Planarity : 0.004 0.063 1557 Dihedral : 6.444 76.049 1316 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.64 % Allowed : 18.98 % Favored : 78.38 % 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: -0.43 (0.25), residues: 1126 helix: 2.20 (0.27), residues: 382 sheet: -1.03 (0.31), residues: 277 loop : -1.98 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS D 199 PHE 0.014 0.001 PHE E 108 TYR 0.027 0.001 TYR E 235 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.910 Fit side-chains REVERT: A 247 MET cc_start: 0.8643 (mtp) cc_final: 0.8370 (mtp) REVERT: A 275 GLU cc_start: 0.8112 (tp30) cc_final: 0.7672 (mm-30) REVERT: B 19 ARG cc_start: 0.7662 (ttp-170) cc_final: 0.7395 (ttp-170) REVERT: B 175 GLN cc_start: 0.7800 (pt0) cc_final: 0.6829 (pm20) REVERT: B 217 MET cc_start: 0.7299 (ptt) cc_final: 0.6821 (ptm) REVERT: B 280 LYS cc_start: 0.8244 (tptp) cc_final: 0.8033 (tptt) REVERT: B 292 PHE cc_start: 0.8634 (m-10) cc_final: 0.8370 (m-10) REVERT: B 312 ASP cc_start: 0.8381 (t0) cc_final: 0.7841 (t0) REVERT: D 180 MET cc_start: 0.7489 (mmt) cc_final: 0.7265 (mpp) REVERT: D 190 SER cc_start: 0.6932 (m) cc_final: 0.6503 (t) REVERT: D 227 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6497 (mp) REVERT: E 82 GLN cc_start: 0.7334 (tp-100) cc_final: 0.6818 (tp40) REVERT: E 93 MET cc_start: 0.7228 (ttp) cc_final: 0.6300 (ttm) outliers start: 26 outliers final: 21 residues processed: 145 average time/residue: 0.2582 time to fit residues: 50.0355 Evaluate side-chains 143 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9255 Z= 0.170 Angle : 0.501 7.375 12500 Z= 0.256 Chirality : 0.040 0.168 1424 Planarity : 0.003 0.063 1557 Dihedral : 6.235 72.691 1316 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.94 % Allowed : 19.70 % Favored : 77.36 % 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: -0.22 (0.25), residues: 1126 helix: 2.40 (0.27), residues: 381 sheet: -0.89 (0.31), residues: 275 loop : -1.88 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE E 108 TYR 0.025 0.001 TYR E 235 ARG 0.006 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 1.135 Fit side-chains REVERT: A 247 MET cc_start: 0.8652 (mtp) cc_final: 0.8365 (mtp) REVERT: B 19 ARG cc_start: 0.7689 (ttp-170) cc_final: 0.7430 (ttp-170) REVERT: B 76 ASP cc_start: 0.7825 (p0) cc_final: 0.7579 (p0) REVERT: B 217 MET cc_start: 0.7299 (ptt) cc_final: 0.6823 (ptm) REVERT: B 280 LYS cc_start: 0.8254 (tptp) cc_final: 0.7939 (tptt) REVERT: B 292 PHE cc_start: 0.8602 (m-10) cc_final: 0.8366 (m-10) REVERT: B 308 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7994 (mt) REVERT: B 312 ASP cc_start: 0.8371 (t0) cc_final: 0.7867 (t0) REVERT: D 180 MET cc_start: 0.7518 (mmt) cc_final: 0.7312 (mpp) REVERT: D 190 SER cc_start: 0.6850 (m) cc_final: 0.6446 (t) REVERT: D 227 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6514 (mp) REVERT: E 82 GLN cc_start: 0.7333 (tp-100) cc_final: 0.6826 (tp40) outliers start: 29 outliers final: 22 residues processed: 149 average time/residue: 0.2273 time to fit residues: 46.2527 Evaluate side-chains 149 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9255 Z= 0.141 Angle : 0.480 7.444 12500 Z= 0.246 Chirality : 0.039 0.163 1424 Planarity : 0.003 0.063 1557 Dihedral : 5.929 69.601 1316 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.94 % Allowed : 19.90 % Favored : 77.16 % 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: -0.01 (0.26), residues: 1126 helix: 2.56 (0.27), residues: 380 sheet: -0.79 (0.32), residues: 275 loop : -1.73 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.002 0.000 HIS E 35 PHE 0.014 0.001 PHE E 108 TYR 0.023 0.001 TYR E 235 ARG 0.006 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.074 Fit side-chains REVERT: A 247 MET cc_start: 0.8640 (mtp) cc_final: 0.8353 (mtp) REVERT: B 19 ARG cc_start: 0.7732 (ttp-170) cc_final: 0.7480 (ttp-170) REVERT: B 172 GLU cc_start: 0.8374 (tt0) cc_final: 0.8135 (tt0) REVERT: B 175 GLN cc_start: 0.7914 (pt0) cc_final: 0.7023 (pm20) REVERT: B 217 MET cc_start: 0.7336 (ptt) cc_final: 0.6793 (ptm) REVERT: B 280 LYS cc_start: 0.8217 (tptp) cc_final: 0.8013 (tptt) REVERT: B 292 PHE cc_start: 0.8499 (m-10) cc_final: 0.8222 (m-10) REVERT: B 312 ASP cc_start: 0.8378 (t0) cc_final: 0.7880 (t0) REVERT: D 151 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6634 (tt) REVERT: D 180 MET cc_start: 0.7545 (mmt) cc_final: 0.7336 (mpp) REVERT: D 190 SER cc_start: 0.6737 (m) cc_final: 0.6363 (t) REVERT: E 82 GLN cc_start: 0.7343 (tp-100) cc_final: 0.6851 (tp40) REVERT: E 93 MET cc_start: 0.7194 (ttp) cc_final: 0.6374 (ttm) outliers start: 29 outliers final: 20 residues processed: 159 average time/residue: 0.2340 time to fit residues: 50.8800 Evaluate side-chains 152 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9255 Z= 0.168 Angle : 0.515 8.421 12500 Z= 0.260 Chirality : 0.040 0.175 1424 Planarity : 0.003 0.063 1557 Dihedral : 5.903 68.295 1316 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.45 % Allowed : 20.61 % Favored : 75.94 % 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: 0.03 (0.26), residues: 1126 helix: 2.54 (0.27), residues: 381 sheet: -0.71 (0.32), residues: 275 loop : -1.71 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE E 108 TYR 0.023 0.001 TYR E 235 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 1.216 Fit side-chains REVERT: A 247 MET cc_start: 0.8651 (mtp) cc_final: 0.8351 (mtp) REVERT: A 306 GLN cc_start: 0.7737 (tp40) cc_final: 0.7438 (tp40) REVERT: B 19 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7491 (ttp-170) REVERT: B 118 ASP cc_start: 0.7863 (t0) cc_final: 0.7579 (t0) REVERT: B 172 GLU cc_start: 0.8369 (tt0) cc_final: 0.8152 (tt0) REVERT: B 175 GLN cc_start: 0.7942 (pt0) cc_final: 0.7026 (pm20) REVERT: B 217 MET cc_start: 0.7380 (ptt) cc_final: 0.6869 (ptm) REVERT: B 280 LYS cc_start: 0.8166 (tptp) cc_final: 0.7964 (tptt) REVERT: B 292 PHE cc_start: 0.8517 (m-10) cc_final: 0.8236 (m-10) REVERT: B 312 ASP cc_start: 0.8375 (t0) cc_final: 0.7872 (t0) REVERT: D 151 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6634 (tt) REVERT: D 190 SER cc_start: 0.6669 (m) cc_final: 0.6334 (t) REVERT: E 82 GLN cc_start: 0.7327 (tp-100) cc_final: 0.6840 (tp40) REVERT: E 93 MET cc_start: 0.7229 (ttp) cc_final: 0.6316 (ttm) outliers start: 34 outliers final: 28 residues processed: 146 average time/residue: 0.2476 time to fit residues: 50.2089 Evaluate side-chains 153 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 68 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 269 ASN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9255 Z= 0.233 Angle : 0.547 8.671 12500 Z= 0.280 Chirality : 0.041 0.168 1424 Planarity : 0.004 0.064 1557 Dihedral : 6.043 70.557 1316 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.76 % Allowed : 20.30 % Favored : 75.94 % 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: -0.04 (0.26), residues: 1126 helix: 2.49 (0.27), residues: 381 sheet: -0.84 (0.31), residues: 284 loop : -1.70 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.017 0.001 PHE E 108 TYR 0.026 0.001 TYR E 235 ARG 0.007 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.945 Fit side-chains REVERT: A 247 MET cc_start: 0.8656 (mtp) cc_final: 0.8343 (mtp) REVERT: A 306 GLN cc_start: 0.7754 (tp40) cc_final: 0.7448 (tp40) REVERT: B 19 ARG cc_start: 0.7751 (ttp-170) cc_final: 0.7511 (ttp-170) REVERT: B 118 ASP cc_start: 0.7933 (t0) cc_final: 0.7652 (t0) REVERT: B 172 GLU cc_start: 0.8406 (tt0) cc_final: 0.8185 (tt0) REVERT: B 175 GLN cc_start: 0.7979 (pt0) cc_final: 0.7046 (pm20) REVERT: B 217 MET cc_start: 0.7380 (ptt) cc_final: 0.6865 (ptm) REVERT: B 280 LYS cc_start: 0.8241 (tptp) cc_final: 0.8031 (tptt) REVERT: B 292 PHE cc_start: 0.8619 (m-10) cc_final: 0.8370 (m-10) REVERT: B 312 ASP cc_start: 0.8369 (t0) cc_final: 0.7817 (t0) REVERT: D 151 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6799 (tt) REVERT: D 190 SER cc_start: 0.6644 (m) cc_final: 0.6405 (t) REVERT: E 82 GLN cc_start: 0.7285 (tp-100) cc_final: 0.6793 (tp40) REVERT: E 93 MET cc_start: 0.7254 (ttp) cc_final: 0.6339 (ttm) outliers start: 37 outliers final: 28 residues processed: 145 average time/residue: 0.2323 time to fit residues: 46.1642 Evaluate side-chains 148 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.0370 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 9255 Z= 0.162 Angle : 0.517 9.090 12500 Z= 0.264 Chirality : 0.040 0.161 1424 Planarity : 0.003 0.061 1557 Dihedral : 5.707 68.999 1316 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.84 % Allowed : 20.71 % Favored : 76.45 % 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: 0.08 (0.26), residues: 1126 helix: 2.58 (0.27), residues: 384 sheet: -0.67 (0.32), residues: 278 loop : -1.71 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.002 0.000 HIS E 35 PHE 0.016 0.001 PHE E 108 TYR 0.024 0.001 TYR E 235 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.001 Fit side-chains REVERT: A 247 MET cc_start: 0.8653 (mtp) cc_final: 0.8340 (mtp) REVERT: A 306 GLN cc_start: 0.7747 (tp40) cc_final: 0.7437 (tp40) REVERT: B 19 ARG cc_start: 0.7769 (ttp-170) cc_final: 0.7531 (ttp-170) REVERT: B 118 ASP cc_start: 0.7903 (t0) cc_final: 0.7595 (t0) REVERT: B 172 GLU cc_start: 0.8377 (tt0) cc_final: 0.8159 (tt0) REVERT: B 175 GLN cc_start: 0.7949 (pt0) cc_final: 0.6983 (pm20) REVERT: B 217 MET cc_start: 0.7419 (ptt) cc_final: 0.6909 (ptm) REVERT: B 234 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7693 (t80) REVERT: B 280 LYS cc_start: 0.8173 (tptp) cc_final: 0.7964 (tptt) REVERT: B 292 PHE cc_start: 0.8502 (m-10) cc_final: 0.8276 (m-10) REVERT: B 312 ASP cc_start: 0.8370 (t0) cc_final: 0.7911 (t0) REVERT: C 42 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7172 (mm-30) REVERT: D 151 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6723 (tt) REVERT: D 190 SER cc_start: 0.7242 (m) cc_final: 0.6872 (t) REVERT: E 82 GLN cc_start: 0.7280 (tp-100) cc_final: 0.6790 (tp40) REVERT: E 93 MET cc_start: 0.7157 (ttp) cc_final: 0.6308 (ttm) REVERT: E 192 MET cc_start: 0.6881 (mmt) cc_final: 0.4327 (ptp) outliers start: 28 outliers final: 25 residues processed: 144 average time/residue: 0.2344 time to fit residues: 46.1723 Evaluate side-chains 153 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.0030 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 9255 Z= 0.148 Angle : 0.502 8.816 12500 Z= 0.256 Chirality : 0.039 0.152 1424 Planarity : 0.004 0.062 1557 Dihedral : 5.199 62.732 1316 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.64 % Allowed : 21.22 % Favored : 76.14 % 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: 0.19 (0.26), residues: 1126 helix: 2.69 (0.27), residues: 383 sheet: -0.58 (0.32), residues: 278 loop : -1.70 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.002 0.000 HIS E 35 PHE 0.016 0.001 PHE E 108 TYR 0.023 0.001 TYR E 235 ARG 0.007 0.000 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.102 Fit side-chains REVERT: A 247 MET cc_start: 0.8626 (mtp) cc_final: 0.8324 (mtp) REVERT: B 19 ARG cc_start: 0.7773 (ttp-170) cc_final: 0.7545 (ttp-170) REVERT: B 118 ASP cc_start: 0.7889 (t0) cc_final: 0.7568 (t0) REVERT: B 172 GLU cc_start: 0.8413 (tt0) cc_final: 0.8196 (tt0) REVERT: B 175 GLN cc_start: 0.7938 (pt0) cc_final: 0.6981 (pm20) REVERT: B 217 MET cc_start: 0.7554 (ptt) cc_final: 0.6994 (ptm) REVERT: B 280 LYS cc_start: 0.8148 (tptp) cc_final: 0.7941 (tptt) REVERT: B 292 PHE cc_start: 0.8445 (m-10) cc_final: 0.8180 (m-10) REVERT: B 312 ASP cc_start: 0.8383 (t0) cc_final: 0.7908 (t0) REVERT: C 42 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7165 (mm-30) REVERT: D 151 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6608 (tt) REVERT: D 190 SER cc_start: 0.7448 (m) cc_final: 0.7198 (t) REVERT: E 82 GLN cc_start: 0.7257 (tp-100) cc_final: 0.6743 (tp40) REVERT: E 93 MET cc_start: 0.7159 (ttp) cc_final: 0.6282 (ttm) REVERT: E 192 MET cc_start: 0.6721 (mmt) cc_final: 0.4201 (ptp) outliers start: 26 outliers final: 25 residues processed: 150 average time/residue: 0.2348 time to fit residues: 47.7215 Evaluate side-chains 158 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.0050 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** D 63 ASN ** 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 = 0.3945 r_free = 0.3945 target = 0.169260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110875 restraints weight = 10027.396| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.43 r_work: 0.3173 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9255 Z= 0.190 Angle : 0.531 9.713 12500 Z= 0.269 Chirality : 0.040 0.168 1424 Planarity : 0.004 0.062 1557 Dihedral : 5.272 63.054 1316 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.94 % Allowed : 21.02 % Favored : 76.04 % 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: 0.14 (0.26), residues: 1126 helix: 2.68 (0.26), residues: 381 sheet: -0.61 (0.32), residues: 279 loop : -1.73 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS E 35 PHE 0.016 0.001 PHE E 108 TYR 0.024 0.001 TYR E 235 ARG 0.007 0.000 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2146.99 seconds wall clock time: 40 minutes 18.82 seconds (2418.82 seconds total)