Starting phenix.real_space_refine on Tue Jul 29 03:49:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7evz_31342/07_2025/7evz_31342.cif Found real_map, /net/cci-nas-00/data/ceres_data/7evz_31342/07_2025/7evz_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_31342/07_2025/7evz_31342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7evz_31342/07_2025/7evz_31342.map" model { file = "/net/cci-nas-00/data/ceres_data/7evz_31342/07_2025/7evz_31342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7evz_31342/07_2025/7evz_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.80, per 1000 atoms: 0.64 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: 2.54 Conformation dependent library (CDL) restraints added in 1.2 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: 1.05 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: 2.72 Time building geometry restraints manager: 2.93 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 25.250 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.670 ------------------------------------------------------------------------------- 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 9258 Z= 0.229 Angle : 0.585 11.711 12506 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 Details of bonding type rmsd hydrogen bonds : bond 0.18619 ( 398) hydrogen bonds : angle 6.32723 ( 1149) SS BOND : bond 0.00065 ( 3) SS BOND : angle 0.84701 ( 6) covalent geometry : bond 0.00443 ( 9255) covalent geometry : angle 0.58492 (12500) *********************** 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 : 1.067 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: 0.2870 time to fit residues: 57.6233 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 : 1.024 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.177133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119747 restraints weight = 10181.089| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.37 r_work: 0.3255 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 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 9258 Z= 0.179 Angle : 0.572 7.532 12506 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 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 398) hydrogen bonds : angle 4.45855 ( 1149) SS BOND : bond 0.00313 ( 3) SS BOND : angle 0.77764 ( 6) covalent geometry : bond 0.00428 ( 9255) covalent geometry : angle 0.57190 (12500) *********************** 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 : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7803 (mtp) cc_final: 0.7555 (mtp) REVERT: A 275 GLU cc_start: 0.7799 (tp30) cc_final: 0.7368 (mm-30) REVERT: B 197 ARG cc_start: 0.6766 (tpp80) cc_final: 0.6532 (tpp80) REVERT: B 217 MET cc_start: 0.6511 (ptt) cc_final: 0.6193 (ptm) REVERT: B 274 THR cc_start: 0.8370 (m) cc_final: 0.7866 (p) REVERT: B 292 PHE cc_start: 0.8117 (m-10) cc_final: 0.7792 (m-10) REVERT: B 312 ASP cc_start: 0.8388 (t0) cc_final: 0.7734 (t0) REVERT: E 82 GLN cc_start: 0.6878 (tp-100) cc_final: 0.6610 (tp40) REVERT: E 93 MET cc_start: 0.5814 (ttm) cc_final: 0.5264 (ttm) REVERT: E 140 MET cc_start: 0.8195 (mmm) cc_final: 0.7726 (mmm) outliers start: 13 outliers final: 8 residues processed: 140 average time/residue: 0.2761 time to fit residues: 50.5827 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 : 1.013 ------------------------------------------------------------------------------- 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 13 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 27 optimal weight: 0.2980 chunk 76 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.178692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120626 restraints weight = 10328.070| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.45 r_work: 0.3259 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9258 Z= 0.137 Angle : 0.519 7.859 12506 Z= 0.268 Chirality : 0.041 0.172 1424 Planarity : 0.004 0.062 1557 Dihedral : 5.828 73.206 1316 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.54 % Allowed : 15.94 % Favored : 81.52 % 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: -0.55 (0.25), residues: 1126 helix: 2.06 (0.27), residues: 382 sheet: -1.05 (0.31), residues: 277 loop : -2.05 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 176 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE A 189 TYR 0.022 0.001 TYR E 235 ARG 0.005 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 398) hydrogen bonds : angle 4.10823 ( 1149) SS BOND : bond 0.00415 ( 3) SS BOND : angle 1.31239 ( 6) covalent geometry : bond 0.00321 ( 9255) covalent geometry : angle 0.51800 (12500) *********************** 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 160 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7817 (mtp) cc_final: 0.7575 (mtp) REVERT: A 275 GLU cc_start: 0.7783 (tp30) cc_final: 0.7301 (mm-30) REVERT: B 175 GLN cc_start: 0.7117 (pt0) cc_final: 0.6082 (pm20) REVERT: B 217 MET cc_start: 0.6544 (ptt) cc_final: 0.6223 (ptm) REVERT: B 274 THR cc_start: 0.8337 (m) cc_final: 0.7873 (p) REVERT: B 292 PHE cc_start: 0.8063 (m-10) cc_final: 0.7856 (m-10) REVERT: B 312 ASP cc_start: 0.8402 (t0) cc_final: 0.7760 (t0) REVERT: D 151 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6258 (tt) REVERT: D 180 MET cc_start: 0.6896 (mmt) cc_final: 0.6674 (mpp) REVERT: D 190 SER cc_start: 0.6056 (m) cc_final: 0.5596 (t) REVERT: E 82 GLN cc_start: 0.6902 (tp-100) cc_final: 0.6628 (tp40) REVERT: E 140 MET cc_start: 0.8133 (mmm) cc_final: 0.7651 (mmm) outliers start: 25 outliers final: 19 residues processed: 151 average time/residue: 0.2436 time to fit residues: 49.4746 Evaluate side-chains 149 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 212 ILE 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 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 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 102 optimal weight: 50.0000 chunk 90 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 29 optimal weight: 0.4980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 6 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.176226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117982 restraints weight = 10367.357| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.52 r_work: 0.3210 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9258 Z= 0.153 Angle : 0.532 7.444 12506 Z= 0.274 Chirality : 0.041 0.180 1424 Planarity : 0.004 0.064 1557 Dihedral : 6.308 73.596 1316 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.94 % Allowed : 18.27 % Favored : 78.78 % 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: -0.38 (0.25), residues: 1126 helix: 2.22 (0.27), residues: 383 sheet: -1.07 (0.31), residues: 282 loop : -1.89 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS D 199 PHE 0.013 0.001 PHE A 189 TYR 0.025 0.001 TYR E 235 ARG 0.006 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 398) hydrogen bonds : angle 4.03153 ( 1149) SS BOND : bond 0.00369 ( 3) SS BOND : angle 1.14611 ( 6) covalent geometry : bond 0.00363 ( 9255) covalent geometry : angle 0.53188 (12500) *********************** 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 162 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.372 Fit side-chains REVERT: A 247 MET cc_start: 0.7827 (mtp) cc_final: 0.7575 (mtp) REVERT: A 275 GLU cc_start: 0.7804 (tp30) cc_final: 0.7323 (mm-30) REVERT: B 19 ARG cc_start: 0.7274 (ttp-170) cc_final: 0.6656 (ttp80) REVERT: B 217 MET cc_start: 0.6647 (ptt) cc_final: 0.6333 (ptm) REVERT: B 292 PHE cc_start: 0.8159 (m-10) cc_final: 0.7909 (m-10) REVERT: B 312 ASP cc_start: 0.8446 (t0) cc_final: 0.7730 (t0) REVERT: D 151 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6307 (tt) REVERT: D 180 MET cc_start: 0.7160 (mmt) cc_final: 0.6952 (mpp) REVERT: D 190 SER cc_start: 0.6187 (m) cc_final: 0.5734 (t) REVERT: E 82 GLN cc_start: 0.6890 (tp-100) cc_final: 0.6443 (tp40) REVERT: E 93 MET cc_start: 0.6026 (ttp) cc_final: 0.5301 (ttm) outliers start: 29 outliers final: 22 residues processed: 153 average time/residue: 0.3158 time to fit residues: 65.9797 Evaluate side-chains 150 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 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 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 312 THR 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 22 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 0.0000 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- 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 B 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.178466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120806 restraints weight = 10283.049| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.49 r_work: 0.3255 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9258 Z= 0.107 Angle : 0.495 7.551 12506 Z= 0.252 Chirality : 0.039 0.167 1424 Planarity : 0.003 0.062 1557 Dihedral : 6.034 70.402 1316 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.94 % Allowed : 18.78 % Favored : 78.27 % 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: -0.15 (0.25), residues: 1126 helix: 2.46 (0.27), residues: 381 sheet: -0.86 (0.32), residues: 277 loop : -1.85 (0.26), residues: 468 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 0.013 0.001 PHE E 108 TYR 0.023 0.001 TYR E 235 ARG 0.006 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 398) hydrogen bonds : angle 3.80728 ( 1149) SS BOND : bond 0.00225 ( 3) SS BOND : angle 0.82772 ( 6) covalent geometry : bond 0.00243 ( 9255) covalent geometry : angle 0.49463 (12500) *********************** 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 160 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.211 Fit side-chains REVERT: A 247 MET cc_start: 0.7855 (mtp) cc_final: 0.7603 (mtp) REVERT: B 19 ARG cc_start: 0.7347 (ttp-170) cc_final: 0.7125 (ttp-170) REVERT: B 175 GLN cc_start: 0.7415 (pt0) cc_final: 0.6396 (pm20) REVERT: B 217 MET cc_start: 0.6696 (ptt) cc_final: 0.6370 (ptm) REVERT: B 292 PHE cc_start: 0.8029 (m-10) cc_final: 0.7795 (m-10) REVERT: B 312 ASP cc_start: 0.8466 (t0) cc_final: 0.7781 (t0) REVERT: D 151 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6284 (tt) REVERT: D 190 SER cc_start: 0.6061 (m) cc_final: 0.5648 (t) REVERT: E 82 GLN cc_start: 0.6864 (tp-100) cc_final: 0.6421 (tp40) outliers start: 29 outliers final: 22 residues processed: 149 average time/residue: 0.2955 time to fit residues: 59.8114 Evaluate side-chains 147 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain A residue 225 VAL 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 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 151 LEU 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 109 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.177283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118992 restraints weight = 10242.411| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.51 r_work: 0.3237 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9258 Z= 0.128 Angle : 0.516 8.266 12506 Z= 0.263 Chirality : 0.040 0.175 1424 Planarity : 0.004 0.063 1557 Dihedral : 6.069 70.595 1316 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.05 % Allowed : 19.49 % Favored : 77.46 % 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: -0.07 (0.26), residues: 1126 helix: 2.50 (0.27), residues: 380 sheet: -0.84 (0.32), residues: 276 loop : -1.75 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE E 108 TYR 0.024 0.001 TYR E 235 ARG 0.006 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 398) hydrogen bonds : angle 3.83361 ( 1149) SS BOND : bond 0.00237 ( 3) SS BOND : angle 0.82236 ( 6) covalent geometry : bond 0.00302 ( 9255) covalent geometry : angle 0.51588 (12500) *********************** 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 156 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.976 Fit side-chains REVERT: A 247 MET cc_start: 0.7880 (mtp) cc_final: 0.7611 (mtp) REVERT: A 275 GLU cc_start: 0.7935 (tp30) cc_final: 0.7709 (mm-30) REVERT: A 306 GLN cc_start: 0.7304 (tp40) cc_final: 0.7049 (tp40) REVERT: B 19 ARG cc_start: 0.7379 (ttp-170) cc_final: 0.7167 (ttp-170) REVERT: B 118 ASP cc_start: 0.8174 (t0) cc_final: 0.7852 (t0) REVERT: B 172 GLU cc_start: 0.8627 (tt0) cc_final: 0.8366 (tt0) REVERT: B 175 GLN cc_start: 0.7423 (pt0) cc_final: 0.6382 (pm20) REVERT: B 217 MET cc_start: 0.6644 (ptt) cc_final: 0.6327 (ptm) REVERT: B 292 PHE cc_start: 0.8090 (m-10) cc_final: 0.7833 (m-10) REVERT: B 312 ASP cc_start: 0.8407 (t0) cc_final: 0.7726 (t0) REVERT: D 151 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6311 (tt) REVERT: D 190 SER cc_start: 0.6008 (m) cc_final: 0.5635 (t) REVERT: E 82 GLN cc_start: 0.6889 (tp-100) cc_final: 0.6441 (tp40) REVERT: E 93 MET cc_start: 0.5993 (ttp) cc_final: 0.5477 (ttm) outliers start: 30 outliers final: 25 residues processed: 144 average time/residue: 0.2290 time to fit residues: 44.8950 Evaluate side-chains 152 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.0670 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 overall best weight: 1.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 346 ASN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.165410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106370 restraints weight = 10195.963| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.47 r_work: 0.3111 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9258 Z= 0.179 Angle : 0.566 8.709 12506 Z= 0.291 Chirality : 0.042 0.181 1424 Planarity : 0.004 0.064 1557 Dihedral : 6.402 73.721 1316 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.55 % Allowed : 20.00 % 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: -0.17 (0.26), residues: 1126 helix: 2.41 (0.27), residues: 381 sheet: -0.95 (0.31), residues: 280 loop : -1.76 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.016 0.001 PHE E 108 TYR 0.028 0.002 TYR E 235 ARG 0.007 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 398) hydrogen bonds : angle 3.99593 ( 1149) SS BOND : bond 0.00303 ( 3) SS BOND : angle 0.98774 ( 6) covalent geometry : bond 0.00432 ( 9255) covalent geometry : angle 0.56615 (12500) *********************** 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 160 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.974 Fit side-chains REVERT: A 247 MET cc_start: 0.8020 (mtp) cc_final: 0.7709 (mtp) REVERT: B 19 ARG cc_start: 0.7442 (ttp-170) cc_final: 0.7230 (ttp-170) REVERT: B 118 ASP cc_start: 0.8263 (t0) cc_final: 0.7980 (t0) REVERT: B 172 GLU cc_start: 0.8718 (tt0) cc_final: 0.8465 (tt0) REVERT: B 175 GLN cc_start: 0.7670 (pt0) cc_final: 0.6589 (pm20) REVERT: B 217 MET cc_start: 0.6902 (ptt) cc_final: 0.6560 (ptm) REVERT: B 292 PHE cc_start: 0.8295 (m-10) cc_final: 0.8004 (m-10) REVERT: B 312 ASP cc_start: 0.8493 (t0) cc_final: 0.7764 (t0) REVERT: D 190 SER cc_start: 0.6063 (m) cc_final: 0.5705 (t) REVERT: E 82 GLN cc_start: 0.6949 (tp-100) cc_final: 0.6477 (tp40) REVERT: E 93 MET cc_start: 0.6279 (ttp) cc_final: 0.5579 (ttm) REVERT: E 192 MET cc_start: 0.7212 (mmt) cc_final: 0.6807 (mmt) outliers start: 35 outliers final: 26 residues processed: 150 average time/residue: 0.2367 time to fit residues: 48.3208 Evaluate side-chains 148 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 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 193 THR 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 3 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.169043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110855 restraints weight = 10162.365| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.44 r_work: 0.3174 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9258 Z= 0.112 Angle : 0.525 8.778 12506 Z= 0.266 Chirality : 0.040 0.161 1424 Planarity : 0.004 0.062 1557 Dihedral : 6.110 71.889 1316 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.74 % Allowed : 20.71 % Favored : 76.55 % 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: -0.02 (0.26), residues: 1126 helix: 2.54 (0.27), residues: 380 sheet: -0.78 (0.32), residues: 275 loop : -1.74 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.000 HIS E 35 PHE 0.015 0.001 PHE E 108 TYR 0.026 0.001 TYR E 235 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 398) hydrogen bonds : angle 3.80573 ( 1149) SS BOND : bond 0.00215 ( 3) SS BOND : angle 2.19036 ( 6) covalent geometry : bond 0.00257 ( 9255) covalent geometry : angle 0.52281 (12500) *********************** 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 152 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.042 Fit side-chains REVERT: A 247 MET cc_start: 0.7977 (mtp) cc_final: 0.7730 (mtp) REVERT: A 306 GLN cc_start: 0.7345 (tp40) cc_final: 0.7096 (tp40) REVERT: B 19 ARG cc_start: 0.7448 (ttp-170) cc_final: 0.7240 (ttp-170) REVERT: B 118 ASP cc_start: 0.8253 (t0) cc_final: 0.7947 (t0) REVERT: B 172 GLU cc_start: 0.8700 (tt0) cc_final: 0.8438 (tt0) REVERT: B 175 GLN cc_start: 0.7603 (pt0) cc_final: 0.6482 (pm20) REVERT: B 217 MET cc_start: 0.6943 (ptt) cc_final: 0.6588 (ptm) REVERT: B 292 PHE cc_start: 0.8147 (m-10) cc_final: 0.7884 (m-10) REVERT: B 312 ASP cc_start: 0.8472 (t0) cc_final: 0.7796 (t0) REVERT: D 180 MET cc_start: 0.7270 (mpp) cc_final: 0.7043 (mpp) REVERT: D 190 SER cc_start: 0.5960 (m) cc_final: 0.5713 (t) REVERT: E 82 GLN cc_start: 0.6927 (tp-100) cc_final: 0.6473 (tp40) REVERT: E 93 MET cc_start: 0.6233 (ttp) cc_final: 0.5558 (ttm) REVERT: E 192 MET cc_start: 0.7083 (mmt) cc_final: 0.6679 (mmt) outliers start: 27 outliers final: 24 residues processed: 143 average time/residue: 0.2302 time to fit residues: 44.9175 Evaluate side-chains 148 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.170050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112156 restraints weight = 9991.851| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.42 r_work: 0.3191 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 9258 Z= 0.105 Angle : 0.518 8.976 12506 Z= 0.263 Chirality : 0.039 0.157 1424 Planarity : 0.004 0.063 1557 Dihedral : 5.777 68.295 1316 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.54 % Allowed : 21.12 % Favored : 76.35 % 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: 0.06 (0.26), residues: 1126 helix: 2.61 (0.27), residues: 381 sheet: -0.70 (0.32), residues: 278 loop : -1.74 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 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 A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 398) hydrogen bonds : angle 3.72935 ( 1149) SS BOND : bond 0.00306 ( 3) SS BOND : angle 1.92542 ( 6) covalent geometry : bond 0.00238 ( 9255) covalent geometry : angle 0.51652 (12500) *********************** 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 152 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.066 Fit side-chains REVERT: A 247 MET cc_start: 0.7978 (mtp) cc_final: 0.7728 (mtp) REVERT: A 306 GLN cc_start: 0.7369 (tp40) cc_final: 0.7112 (tp40) REVERT: B 19 ARG cc_start: 0.7455 (ttp-170) cc_final: 0.7249 (ttp-170) REVERT: B 118 ASP cc_start: 0.8223 (t0) cc_final: 0.7885 (t0) REVERT: B 172 GLU cc_start: 0.8716 (tt0) cc_final: 0.8452 (tt0) REVERT: B 175 GLN cc_start: 0.7616 (pt0) cc_final: 0.6506 (pm20) REVERT: B 217 MET cc_start: 0.7007 (ptt) cc_final: 0.6624 (ptm) REVERT: B 234 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7453 (t80) REVERT: B 292 PHE cc_start: 0.8148 (m-10) cc_final: 0.7824 (m-10) REVERT: B 312 ASP cc_start: 0.8476 (t0) cc_final: 0.7797 (t0) REVERT: D 190 SER cc_start: 0.6914 (m) cc_final: 0.6539 (t) REVERT: E 82 GLN cc_start: 0.6912 (tp-100) cc_final: 0.6433 (tp40) REVERT: E 93 MET cc_start: 0.6281 (ttp) cc_final: 0.5581 (ttm) REVERT: E 192 MET cc_start: 0.7003 (mmt) cc_final: 0.6644 (mmt) outliers start: 25 outliers final: 22 residues processed: 139 average time/residue: 0.2299 time to fit residues: 43.6136 Evaluate side-chains 148 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.169331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111280 restraints weight = 10159.390| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.44 r_work: 0.3189 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9258 Z= 0.114 Angle : 0.530 8.687 12506 Z= 0.268 Chirality : 0.040 0.162 1424 Planarity : 0.004 0.063 1557 Dihedral : 5.585 66.799 1316 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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: 0.07 (0.26), residues: 1126 helix: 2.63 (0.27), residues: 381 sheet: -0.68 (0.32), residues: 278 loop : -1.75 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 PHE 0.017 0.001 PHE E 108 TYR 0.025 0.001 TYR E 235 ARG 0.007 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 398) hydrogen bonds : angle 3.73472 ( 1149) SS BOND : bond 0.00218 ( 3) SS BOND : angle 1.81048 ( 6) covalent geometry : bond 0.00267 ( 9255) covalent geometry : angle 0.52848 (12500) ********************** 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 152 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.549 Fit side-chains REVERT: A 247 MET cc_start: 0.8045 (mtp) cc_final: 0.7794 (mtp) REVERT: A 306 GLN cc_start: 0.7409 (tp40) cc_final: 0.7145 (tp40) REVERT: B 19 ARG cc_start: 0.7483 (ttp-170) cc_final: 0.7277 (ttp-170) REVERT: B 118 ASP cc_start: 0.8256 (t0) cc_final: 0.7926 (t0) REVERT: B 172 GLU cc_start: 0.8744 (tt0) cc_final: 0.8485 (tt0) REVERT: B 175 GLN cc_start: 0.7686 (pt0) cc_final: 0.6569 (pm20) REVERT: B 217 MET cc_start: 0.7311 (ptt) cc_final: 0.6896 (ptm) REVERT: B 234 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7506 (t80) REVERT: B 292 PHE cc_start: 0.8195 (m-10) cc_final: 0.7874 (m-10) REVERT: B 312 ASP cc_start: 0.8492 (t0) cc_final: 0.7817 (t0) REVERT: C 42 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7038 (mm-30) REVERT: D 190 SER cc_start: 0.7015 (m) cc_final: 0.6707 (t) REVERT: E 82 GLN cc_start: 0.6955 (tp-100) cc_final: 0.6476 (tp40) REVERT: E 93 MET cc_start: 0.6421 (ttp) cc_final: 0.5697 (ttm) REVERT: E 192 MET cc_start: 0.7027 (mmt) cc_final: 0.6670 (mmt) outliers start: 26 outliers final: 23 residues processed: 142 average time/residue: 0.3034 time to fit residues: 58.2103 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 : 0.795 ------------------------------------------------------------------------------- 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 263 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 0.8980 chunk 85 optimal weight: 0.0370 chunk 20 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.170952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112843 restraints weight = 10069.245| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.44 r_work: 0.3198 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 9258 Z= 0.102 Angle : 0.517 9.637 12506 Z= 0.261 Chirality : 0.039 0.155 1424 Planarity : 0.003 0.063 1557 Dihedral : 5.246 63.534 1316 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.84 % Allowed : 20.61 % Favored : 76.55 % 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: 2.74 (0.27), residues: 380 sheet: -0.64 (0.32), residues: 278 loop : -1.76 (0.26), residues: 468 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 0.017 0.001 PHE E 108 TYR 0.024 0.001 TYR E 235 ARG 0.007 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 398) hydrogen bonds : angle 3.67215 ( 1149) SS BOND : bond 0.00247 ( 3) SS BOND : angle 1.55692 ( 6) covalent geometry : bond 0.00234 ( 9255) covalent geometry : angle 0.51563 (12500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5523.57 seconds wall clock time: 97 minutes 16.61 seconds (5836.61 seconds total)