Starting phenix.real_space_refine on Sat Aug 23 11:28:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c1z_16385/08_2025/8c1z_16385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c1z_16385/08_2025/8c1z_16385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8c1z_16385/08_2025/8c1z_16385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c1z_16385/08_2025/8c1z_16385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c1z_16385/08_2025/8c1z_16385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c1z_16385/08_2025/8c1z_16385.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 7851 2.51 5 N 1916 2.21 5 O 2064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11863 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 3042 Classifications: {'peptide': 368} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 347} Chain breaks: 1 Chain: "B" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 3035 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Chain: "C" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2988 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain breaks: 4 Chain: "D" Number of atoms: 2798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2798 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 318} Chain breaks: 11 Time building chain proxies: 3.60, per 1000 atoms: 0.30 Number of scatterers: 11863 At special positions: 0 Unit cell: (95.418, 92.907, 127.224, 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 32 16.00 O 2064 8.00 N 1916 7.00 C 7851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " 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: 1.19 Conformation dependent library (CDL) restraints added in 547.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2790 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 44.0% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 removed outlier: 4.301A pdb=" N ASN A 22 " --> pdb=" O HIS A 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.521A pdb=" N ASP A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 227 through 243 removed outlier: 3.722A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 273 removed outlier: 3.565A pdb=" N PHE A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 287 through 311 removed outlier: 3.504A pdb=" N MET A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 333 removed outlier: 3.850A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TRP A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 459 Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.550A pdb=" N HIS B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASN B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.859A pdb=" N ASP B 81 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 241 removed outlier: 3.909A pdb=" N SER B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 273 removed outlier: 3.753A pdb=" N VAL B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 284 through 307 removed outlier: 4.000A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 Processing helix chain 'B' and resid 422 through 462 Processing helix chain 'C' and resid 10 through 22 removed outlier: 4.283A pdb=" N ASN C 22 " --> pdb=" O HIS C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 175 removed outlier: 3.602A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 227 through 244 removed outlier: 3.518A pdb=" N SER C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 273 removed outlier: 3.678A pdb=" N VAL C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 309 removed outlier: 4.048A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 294 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.995A pdb=" N TRP C 320 " --> pdb=" O PRO C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 426 through 462 removed outlier: 3.580A pdb=" N SER C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.502A pdb=" N SER D 92 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE D 93 " --> pdb=" O THR D 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 93' Processing helix chain 'D' and resid 170 through 177 removed outlier: 3.938A pdb=" N ASP D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 Processing helix chain 'D' and resid 227 through 243 removed outlier: 3.671A pdb=" N SER D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 273 removed outlier: 4.240A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR D 272 " --> pdb=" O ILE D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 310 removed outlier: 3.594A pdb=" N PHE D 287 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 removed outlier: 4.038A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 461 removed outlier: 4.314A pdb=" N ASP D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.907A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 52 removed outlier: 6.995A pdb=" N VAL A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 101 removed outlier: 4.621A pdb=" N THR A 152 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 134 removed outlier: 7.174A pdb=" N VAL B 57 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN B 50 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 44 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B 164 " --> pdb=" O THR B 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 88 Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.083A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N TYR B 207 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU B 198 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU B 209 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE B 196 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS B 211 " --> pdb=" O PRO B 194 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N TYR B 213 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL B 192 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 215 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 89 removed outlier: 10.883A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 116 " --> pdb=" O GLN C 124 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL C 132 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 89 removed outlier: 10.883A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 116 " --> pdb=" O GLN C 124 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 152 through 154 removed outlier: 3.580A pdb=" N PHE C 193 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 124 through 128 Processing sheet with id=AB2, first strand: chain 'D' and resid 124 through 128 removed outlier: 7.412A pdb=" N VAL D 57 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASN D 50 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 146 through 153 removed outlier: 6.524A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3610 1.34 - 1.46: 2707 1.46 - 1.58: 5827 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 12192 Sorted by residual: bond pdb=" N VAL D 83 " pdb=" CA VAL D 83 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.68e+00 bond pdb=" N ILE D 278 " pdb=" CA ILE D 278 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.19e-02 7.06e+03 5.97e+00 bond pdb=" N GLN A 147 " pdb=" CA GLN A 147 " ideal model delta sigma weight residual 1.458 1.484 -0.027 1.19e-02 7.06e+03 4.98e+00 bond pdb=" N ASP C 105 " pdb=" CA ASP C 105 " ideal model delta sigma weight residual 1.457 1.431 0.027 1.29e-02 6.01e+03 4.29e+00 bond pdb=" N ASN D 82 " pdb=" CA ASN D 82 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.46e-02 4.69e+03 3.88e+00 ... (remaining 12187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 16301 1.59 - 3.17: 298 3.17 - 4.76: 62 4.76 - 6.35: 3 6.35 - 7.94: 5 Bond angle restraints: 16669 Sorted by residual: angle pdb=" N GLY D 279 " pdb=" CA GLY D 279 " pdb=" C GLY D 279 " ideal model delta sigma weight residual 115.21 107.27 7.94 1.30e+00 5.92e-01 3.73e+01 angle pdb=" N GLN A 147 " pdb=" CA GLN A 147 " pdb=" C GLN A 147 " ideal model delta sigma weight residual 108.41 115.63 -7.22 1.63e+00 3.76e-01 1.96e+01 angle pdb=" N VAL C 106 " pdb=" CA VAL C 106 " pdb=" CB VAL C 106 " ideal model delta sigma weight residual 111.50 105.02 6.48 1.70e+00 3.46e-01 1.45e+01 angle pdb=" N ASP D 81 " pdb=" CA ASP D 81 " pdb=" C ASP D 81 " ideal model delta sigma weight residual 112.58 108.17 4.41 1.22e+00 6.72e-01 1.31e+01 angle pdb=" CA ASN D 82 " pdb=" C ASN D 82 " pdb=" O ASN D 82 " ideal model delta sigma weight residual 121.28 117.33 3.95 1.19e+00 7.06e-01 1.10e+01 ... (remaining 16664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 6181 16.04 - 32.08: 707 32.08 - 48.13: 211 48.13 - 64.17: 38 64.17 - 80.21: 9 Dihedral angle restraints: 7146 sinusoidal: 2877 harmonic: 4269 Sorted by residual: dihedral pdb=" CA TYR A 286 " pdb=" C TYR A 286 " pdb=" N PHE A 287 " pdb=" CA PHE A 287 " ideal model delta harmonic sigma weight residual 180.00 153.11 26.89 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 136.48 -43.48 1 1.00e+01 1.00e-02 2.63e+01 dihedral pdb=" CA PHE A 144 " pdb=" C PHE A 144 " pdb=" N ASP A 145 " pdb=" CA ASP A 145 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 7143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1564 0.048 - 0.096: 288 0.096 - 0.143: 86 0.143 - 0.191: 6 0.191 - 0.239: 3 Chirality restraints: 1947 Sorted by residual: chirality pdb=" CA VAL A 106 " pdb=" N VAL A 106 " pdb=" C VAL A 106 " pdb=" CB VAL A 106 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP C 105 " pdb=" N ASP C 105 " pdb=" C ASP C 105 " pdb=" CB ASP C 105 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL C 106 " pdb=" N VAL C 106 " pdb=" C VAL C 106 " pdb=" CB VAL C 106 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 1944 not shown) Planarity restraints: 2030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 88 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO D 89 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 89 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 89 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 277 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C ALA D 277 " -0.028 2.00e-02 2.50e+03 pdb=" O ALA D 277 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE D 278 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 82 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C ASN D 82 " -0.026 2.00e-02 2.50e+03 pdb=" O ASN D 82 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL D 83 " 0.009 2.00e-02 2.50e+03 ... (remaining 2027 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 65 2.49 - 3.10: 8813 3.10 - 3.70: 18034 3.70 - 4.30: 25423 4.30 - 4.90: 42966 Nonbonded interactions: 95301 Sorted by model distance: nonbonded pdb=" O VAL C 104 " pdb=" OD1 ASP C 105 " model vdw 1.892 3.040 nonbonded pdb=" O VAL A 104 " pdb=" OD1 ASP A 105 " model vdw 2.009 3.040 nonbonded pdb=" OG SER C 170 " pdb=" OE1 GLU C 173 " model vdw 2.219 3.040 nonbonded pdb=" N GLN B 74 " pdb=" OE1 GLN B 74 " model vdw 2.225 3.120 nonbonded pdb=" O LEU C 293 " pdb=" OH TYR C 441 " model vdw 2.230 3.040 ... (remaining 95296 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 22 or resid 27 through 29 or resid 33 or resid \ 39 through 69 or resid 72 through 94 or resid 99 through 106 or resid 109 throug \ h 110 or resid 113 through 116 or resid 118 through 160 or resid 165 through 195 \ or resid 197 through 198 or resid 205 through 462)) selection = (chain 'B' and (resid 12 through 22 or resid 27 through 29 or resid 33 or resid \ 39 through 69 or resid 72 through 94 or resid 99 through 106 or resid 109 throug \ h 110 or resid 113 through 116 or resid 118 through 160 or resid 165 through 195 \ or resid 197 through 198 or resid 205 through 462)) selection = (chain 'C' and (resid 12 through 22 or resid 27 through 29 or resid 33 or resid \ 39 through 69 or resid 72 through 94 or resid 99 through 110 or resid 113 throug \ h 116 or resid 118 through 160 or resid 165 through 195 or resid 197 through 198 \ or resid 205 through 333 or resid 421 through 462)) selection = (chain 'D' and (resid 12 through 22 or resid 27 through 94 or resid 99 through 1 \ 06 or resid 109 through 333 or resid 421 through 462)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.940 Find NCS groups from input model: 0.260 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12196 Z= 0.151 Angle : 0.554 7.935 16677 Z= 0.309 Chirality : 0.043 0.239 1947 Planarity : 0.004 0.040 2030 Dihedral : 15.091 80.208 4344 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.03 % Favored : 94.61 % Rotamer: Outliers : 0.22 % Allowed : 11.94 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.24), residues: 1392 helix: 1.81 (0.23), residues: 552 sheet: -1.86 (0.27), residues: 334 loop : -1.25 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 169 TYR 0.012 0.001 TYR C 67 PHE 0.023 0.001 PHE D 233 TRP 0.019 0.001 TRP C 156 HIS 0.005 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00315 (12192) covalent geometry : angle 0.55376 (16669) SS BOND : bond 0.00145 ( 4) SS BOND : angle 0.47459 ( 8) hydrogen bonds : bond 0.12526 ( 586) hydrogen bonds : angle 6.48477 ( 1734) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 145 average time/residue: 0.1127 time to fit residues: 23.7320 Evaluate side-chains 87 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain D residue 278 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.088930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.061650 restraints weight = 44457.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.063432 restraints weight = 22835.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.064291 restraints weight = 15829.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.065193 restraints weight = 13335.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.065337 restraints weight = 11852.711| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12196 Z= 0.254 Angle : 0.639 7.668 16677 Z= 0.327 Chirality : 0.043 0.166 1947 Planarity : 0.005 0.047 2030 Dihedral : 4.641 47.700 1566 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.32 % Favored : 94.47 % Rotamer: Outliers : 2.76 % Allowed : 13.88 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.24), residues: 1392 helix: 2.24 (0.22), residues: 557 sheet: -1.82 (0.27), residues: 336 loop : -1.16 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.021 0.002 TYR C 67 PHE 0.034 0.002 PHE D 233 TRP 0.014 0.001 TRP C 331 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00576 (12192) covalent geometry : angle 0.63883 (16669) SS BOND : bond 0.00352 ( 4) SS BOND : angle 0.65833 ( 8) hydrogen bonds : bond 0.03788 ( 586) hydrogen bonds : angle 4.76637 ( 1734) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7845 (tm-30) REVERT: A 300 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8558 (tm-30) REVERT: B 54 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8873 (tppt) REVERT: B 86 LEU cc_start: 0.9257 (tt) cc_final: 0.9047 (tt) REVERT: B 235 MET cc_start: 0.8983 (mmt) cc_final: 0.8649 (mmt) REVERT: C 240 VAL cc_start: 0.9520 (OUTLIER) cc_final: 0.9315 (p) outliers start: 37 outliers final: 20 residues processed: 111 average time/residue: 0.1038 time to fit residues: 17.5300 Evaluate side-chains 93 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 433 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 29 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN ** D 125 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 = 0.3731 r_free = 0.3731 target = 0.091326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.064268 restraints weight = 43606.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.066211 restraints weight = 21948.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.067414 restraints weight = 14955.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.067890 restraints weight = 12255.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.068352 restraints weight = 11186.273| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12196 Z= 0.113 Angle : 0.545 8.427 16677 Z= 0.279 Chirality : 0.042 0.175 1947 Planarity : 0.004 0.044 2030 Dihedral : 4.144 23.587 1563 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.81 % Favored : 95.98 % Rotamer: Outliers : 2.01 % Allowed : 16.34 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.24), residues: 1392 helix: 2.79 (0.22), residues: 552 sheet: -1.65 (0.27), residues: 345 loop : -1.04 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 14 TYR 0.021 0.001 TYR C 67 PHE 0.022 0.001 PHE D 233 TRP 0.014 0.001 TRP C 331 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00256 (12192) covalent geometry : angle 0.54467 (16669) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.27180 ( 8) hydrogen bonds : bond 0.03263 ( 586) hydrogen bonds : angle 4.30789 ( 1734) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7792 (tm-30) REVERT: B 54 LYS cc_start: 0.9133 (tptt) cc_final: 0.8832 (tppt) REVERT: B 86 LEU cc_start: 0.9202 (tt) cc_final: 0.8900 (tt) REVERT: D 45 MET cc_start: 0.8303 (mmm) cc_final: 0.7853 (tpp) REVERT: D 118 HIS cc_start: 0.7804 (t70) cc_final: 0.7566 (t70) REVERT: D 235 MET cc_start: 0.8761 (mtp) cc_final: 0.8413 (mmt) outliers start: 27 outliers final: 14 residues processed: 114 average time/residue: 0.1015 time to fit residues: 17.4240 Evaluate side-chains 93 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 433 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 51 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 0.0030 chunk 24 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.089456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.062221 restraints weight = 44161.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064091 restraints weight = 22459.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065221 restraints weight = 15407.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.065694 restraints weight = 12658.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.066201 restraints weight = 11593.425| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12196 Z= 0.179 Angle : 0.576 9.366 16677 Z= 0.291 Chirality : 0.041 0.152 1947 Planarity : 0.004 0.043 2030 Dihedral : 4.128 24.815 1563 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.96 % Favored : 94.83 % Rotamer: Outliers : 2.09 % Allowed : 17.16 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.24), residues: 1392 helix: 2.85 (0.22), residues: 558 sheet: -1.60 (0.28), residues: 336 loop : -0.96 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 14 TYR 0.020 0.001 TYR C 67 PHE 0.021 0.001 PHE D 233 TRP 0.013 0.001 TRP C 331 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00406 (12192) covalent geometry : angle 0.57637 (16669) SS BOND : bond 0.00259 ( 4) SS BOND : angle 0.35611 ( 8) hydrogen bonds : bond 0.03299 ( 586) hydrogen bonds : angle 4.30671 ( 1734) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8648 (t) REVERT: A 188 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7867 (tm-30) REVERT: A 300 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8525 (tm-30) REVERT: B 54 LYS cc_start: 0.9099 (tptt) cc_final: 0.8819 (tppt) REVERT: B 86 LEU cc_start: 0.9184 (tt) cc_final: 0.8817 (tt) REVERT: B 235 MET cc_start: 0.8743 (mmt) cc_final: 0.8273 (mmt) REVERT: D 235 MET cc_start: 0.8734 (mtp) cc_final: 0.8289 (mmt) outliers start: 28 outliers final: 17 residues processed: 101 average time/residue: 0.1044 time to fit residues: 16.0729 Evaluate side-chains 91 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 307 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 77 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 30.0000 chunk 131 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.088884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.061484 restraints weight = 44275.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.063333 restraints weight = 22207.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.064472 restraints weight = 15148.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.064797 restraints weight = 12403.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065347 restraints weight = 11527.562| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12196 Z= 0.188 Angle : 0.573 9.621 16677 Z= 0.290 Chirality : 0.041 0.156 1947 Planarity : 0.004 0.043 2030 Dihedral : 4.138 23.388 1563 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.45 % Favored : 95.33 % Rotamer: Outliers : 3.13 % Allowed : 17.09 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.24), residues: 1392 helix: 2.84 (0.22), residues: 560 sheet: -1.59 (0.28), residues: 335 loop : -0.96 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 251 TYR 0.020 0.001 TYR C 67 PHE 0.012 0.001 PHE D 233 TRP 0.012 0.001 TRP C 331 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00427 (12192) covalent geometry : angle 0.57292 (16669) SS BOND : bond 0.00283 ( 4) SS BOND : angle 0.42098 ( 8) hydrogen bonds : bond 0.03341 ( 586) hydrogen bonds : angle 4.29781 ( 1734) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 75 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8617 (t) REVERT: A 188 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 189 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9082 (tt) REVERT: B 54 LYS cc_start: 0.9063 (tptt) cc_final: 0.8752 (tppt) REVERT: B 86 LEU cc_start: 0.9274 (tt) cc_final: 0.8886 (tt) REVERT: C 35 LYS cc_start: 0.9134 (pptt) cc_final: 0.8842 (pptt) REVERT: D 235 MET cc_start: 0.8736 (mtp) cc_final: 0.8282 (mmt) REVERT: D 263 SER cc_start: 0.9479 (m) cc_final: 0.9164 (p) REVERT: D 309 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7518 (t-170) outliers start: 42 outliers final: 27 residues processed: 110 average time/residue: 0.0948 time to fit residues: 16.4262 Evaluate side-chains 99 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 437 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 7 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 66 optimal weight: 0.0870 chunk 112 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.088302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.060852 restraints weight = 45395.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.062653 restraints weight = 23230.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.063799 restraints weight = 16033.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.064259 restraints weight = 13205.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.064429 restraints weight = 12101.301| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12196 Z= 0.202 Angle : 0.585 8.756 16677 Z= 0.293 Chirality : 0.041 0.154 1947 Planarity : 0.004 0.043 2030 Dihedral : 4.186 23.721 1563 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.03 % Favored : 94.76 % Rotamer: Outliers : 2.84 % Allowed : 18.43 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.24), residues: 1392 helix: 2.83 (0.22), residues: 563 sheet: -1.64 (0.27), residues: 345 loop : -0.90 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.021 0.001 TYR C 67 PHE 0.011 0.001 PHE C 254 TRP 0.012 0.001 TRP C 331 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00459 (12192) covalent geometry : angle 0.58464 (16669) SS BOND : bond 0.00304 ( 4) SS BOND : angle 0.45072 ( 8) hydrogen bonds : bond 0.03351 ( 586) hydrogen bonds : angle 4.34711 ( 1734) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 73 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 189 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9071 (tt) REVERT: A 300 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8509 (tm-30) REVERT: B 54 LYS cc_start: 0.9088 (tptt) cc_final: 0.8764 (tppt) REVERT: B 86 LEU cc_start: 0.9308 (tt) cc_final: 0.8947 (tt) REVERT: C 35 LYS cc_start: 0.9190 (pptt) cc_final: 0.8899 (pptt) REVERT: D 263 SER cc_start: 0.9467 (m) cc_final: 0.9157 (p) outliers start: 38 outliers final: 29 residues processed: 104 average time/residue: 0.0933 time to fit residues: 15.1400 Evaluate side-chains 97 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 307 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 114 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.090136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.063815 restraints weight = 45098.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.065376 restraints weight = 21130.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.065635 restraints weight = 14382.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065951 restraints weight = 14865.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.065897 restraints weight = 13245.108| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12196 Z= 0.116 Angle : 0.543 8.540 16677 Z= 0.272 Chirality : 0.041 0.151 1947 Planarity : 0.003 0.046 2030 Dihedral : 4.063 20.764 1563 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.31 % Favored : 95.47 % Rotamer: Outliers : 2.54 % Allowed : 18.28 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.25), residues: 1392 helix: 3.00 (0.22), residues: 560 sheet: -1.54 (0.28), residues: 341 loop : -0.87 (0.31), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 328 TYR 0.020 0.001 TYR C 67 PHE 0.022 0.001 PHE D 80 TRP 0.014 0.001 TRP C 331 HIS 0.005 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00270 (12192) covalent geometry : angle 0.54286 (16669) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.30829 ( 8) hydrogen bonds : bond 0.03055 ( 586) hydrogen bonds : angle 4.14547 ( 1734) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7832 (tm-30) REVERT: A 189 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9062 (tt) REVERT: A 300 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8494 (tm-30) REVERT: B 54 LYS cc_start: 0.9096 (tptt) cc_final: 0.8731 (tppt) REVERT: C 35 LYS cc_start: 0.9183 (pptt) cc_final: 0.8966 (pptt) REVERT: C 54 LYS cc_start: 0.9176 (tptt) cc_final: 0.8751 (tppt) REVERT: C 291 MET cc_start: 0.8863 (tpp) cc_final: 0.8555 (tmm) REVERT: D 235 MET cc_start: 0.8912 (mmm) cc_final: 0.8613 (mmt) REVERT: D 263 SER cc_start: 0.9450 (m) cc_final: 0.9143 (p) outliers start: 34 outliers final: 25 residues processed: 108 average time/residue: 0.0953 time to fit residues: 16.0549 Evaluate side-chains 97 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 437 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 111 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 87 optimal weight: 0.0020 chunk 97 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 82 optimal weight: 40.0000 chunk 32 optimal weight: 8.9990 chunk 81 optimal weight: 0.4980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.091483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.065326 restraints weight = 44758.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.066731 restraints weight = 22220.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.067134 restraints weight = 15194.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.067442 restraints weight = 15162.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.067558 restraints weight = 13834.901| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12196 Z= 0.100 Angle : 0.553 10.343 16677 Z= 0.271 Chirality : 0.041 0.150 1947 Planarity : 0.003 0.045 2030 Dihedral : 3.925 19.675 1563 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.24 % Favored : 95.55 % Rotamer: Outliers : 2.39 % Allowed : 18.58 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.25), residues: 1392 helix: 3.16 (0.22), residues: 550 sheet: -1.48 (0.27), residues: 348 loop : -0.83 (0.31), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 328 TYR 0.020 0.001 TYR C 67 PHE 0.016 0.001 PHE D 80 TRP 0.015 0.001 TRP C 331 HIS 0.004 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00232 (12192) covalent geometry : angle 0.55302 (16669) SS BOND : bond 0.00092 ( 4) SS BOND : angle 0.27904 ( 8) hydrogen bonds : bond 0.02846 ( 586) hydrogen bonds : angle 4.02593 ( 1734) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 189 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8956 (tt) REVERT: A 300 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8466 (tm-30) REVERT: B 54 LYS cc_start: 0.9044 (tptt) cc_final: 0.8689 (tppt) REVERT: B 86 LEU cc_start: 0.9242 (tp) cc_final: 0.8974 (tt) REVERT: B 235 MET cc_start: 0.8559 (mmt) cc_final: 0.8270 (mmt) REVERT: C 35 LYS cc_start: 0.9198 (pptt) cc_final: 0.8974 (pptt) REVERT: C 54 LYS cc_start: 0.9073 (tptt) cc_final: 0.8694 (tppt) REVERT: D 235 MET cc_start: 0.8927 (mmm) cc_final: 0.8669 (mmt) REVERT: D 263 SER cc_start: 0.9423 (m) cc_final: 0.9130 (p) REVERT: D 287 PHE cc_start: 0.9336 (OUTLIER) cc_final: 0.8926 (t80) outliers start: 32 outliers final: 23 residues processed: 112 average time/residue: 0.0938 time to fit residues: 16.4051 Evaluate side-chains 103 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 307 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 77 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 109 optimal weight: 40.0000 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.090908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.065207 restraints weight = 44941.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.066498 restraints weight = 22513.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.066701 restraints weight = 15423.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067006 restraints weight = 15089.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.067210 restraints weight = 14148.897| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 12196 Z= 0.117 Angle : 0.573 11.564 16677 Z= 0.284 Chirality : 0.042 0.288 1947 Planarity : 0.004 0.045 2030 Dihedral : 3.945 19.164 1563 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.02 % Favored : 95.76 % Rotamer: Outliers : 2.16 % Allowed : 19.48 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.24), residues: 1392 helix: 3.14 (0.22), residues: 550 sheet: -1.44 (0.28), residues: 341 loop : -0.81 (0.30), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 328 TYR 0.020 0.001 TYR C 67 PHE 0.020 0.001 PHE D 80 TRP 0.014 0.001 TRP C 331 HIS 0.004 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00278 (12192) covalent geometry : angle 0.57276 (16669) SS BOND : bond 0.00133 ( 4) SS BOND : angle 0.31653 ( 8) hydrogen bonds : bond 0.02971 ( 586) hydrogen bonds : angle 4.07982 ( 1734) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 189 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8966 (tt) REVERT: B 54 LYS cc_start: 0.9064 (tptt) cc_final: 0.8698 (tppt) REVERT: B 86 LEU cc_start: 0.9235 (tp) cc_final: 0.8955 (tt) REVERT: C 35 LYS cc_start: 0.9211 (pptt) cc_final: 0.9000 (pptt) REVERT: C 54 LYS cc_start: 0.9085 (tptt) cc_final: 0.8708 (tppt) REVERT: C 197 LYS cc_start: 0.9318 (mmmt) cc_final: 0.9008 (mmtm) REVERT: D 235 MET cc_start: 0.8906 (mmm) cc_final: 0.8626 (mmt) REVERT: D 263 SER cc_start: 0.9436 (m) cc_final: 0.9157 (p) REVERT: D 287 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8959 (t80) outliers start: 29 outliers final: 24 residues processed: 103 average time/residue: 0.1010 time to fit residues: 16.0036 Evaluate side-chains 100 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 307 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 40.0000 chunk 94 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 61 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.090784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.063847 restraints weight = 44487.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.065767 restraints weight = 21922.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.067012 restraints weight = 14844.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.067509 restraints weight = 12053.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 13)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.067510 restraints weight = 10996.565| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 12196 Z= 0.115 Angle : 0.580 11.474 16677 Z= 0.284 Chirality : 0.042 0.251 1947 Planarity : 0.004 0.046 2030 Dihedral : 3.891 19.065 1563 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.38 % Favored : 95.40 % Rotamer: Outliers : 2.16 % Allowed : 19.63 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.24), residues: 1392 helix: 3.14 (0.22), residues: 550 sheet: -1.45 (0.27), residues: 348 loop : -0.76 (0.31), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 251 TYR 0.020 0.001 TYR C 67 PHE 0.020 0.001 PHE B 303 TRP 0.014 0.001 TRP C 331 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00273 (12192) covalent geometry : angle 0.57986 (16669) SS BOND : bond 0.00139 ( 4) SS BOND : angle 0.27873 ( 8) hydrogen bonds : bond 0.02953 ( 586) hydrogen bonds : angle 4.05803 ( 1734) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7819 (tm-30) REVERT: A 189 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8959 (tt) REVERT: B 54 LYS cc_start: 0.9063 (tptt) cc_final: 0.8692 (tppt) REVERT: B 86 LEU cc_start: 0.9231 (tp) cc_final: 0.8946 (tt) REVERT: C 35 LYS cc_start: 0.9239 (pptt) cc_final: 0.9026 (pptt) REVERT: C 54 LYS cc_start: 0.9097 (tptt) cc_final: 0.8712 (tppt) REVERT: D 235 MET cc_start: 0.8968 (mmm) cc_final: 0.8695 (mmt) REVERT: D 263 SER cc_start: 0.9444 (m) cc_final: 0.9159 (p) REVERT: D 287 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8967 (t80) outliers start: 29 outliers final: 24 residues processed: 104 average time/residue: 0.0999 time to fit residues: 15.9510 Evaluate side-chains 102 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 307 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 132 optimal weight: 0.0870 chunk 18 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.091080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.064852 restraints weight = 45669.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.066105 restraints weight = 21600.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.066286 restraints weight = 15065.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.067391 restraints weight = 15198.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.067205 restraints weight = 13273.930| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12196 Z= 0.122 Angle : 0.592 14.323 16677 Z= 0.290 Chirality : 0.042 0.240 1947 Planarity : 0.004 0.046 2030 Dihedral : 3.906 19.274 1563 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.17 % Favored : 95.62 % Rotamer: Outliers : 2.09 % Allowed : 19.78 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.24), residues: 1392 helix: 3.13 (0.22), residues: 551 sheet: -1.41 (0.28), residues: 343 loop : -0.75 (0.31), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 251 TYR 0.020 0.001 TYR C 67 PHE 0.020 0.001 PHE B 303 TRP 0.013 0.001 TRP C 331 HIS 0.004 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00286 (12192) covalent geometry : angle 0.59240 (16669) SS BOND : bond 0.00144 ( 4) SS BOND : angle 0.28687 ( 8) hydrogen bonds : bond 0.02967 ( 586) hydrogen bonds : angle 4.03666 ( 1734) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.49 seconds wall clock time: 32 minutes 39.94 seconds (1959.94 seconds total)