Starting phenix.real_space_refine on Wed Mar 4 02:09:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7btw_30189/03_2026/7btw_30189.cif Found real_map, /net/cci-nas-00/data/ceres_data/7btw_30189/03_2026/7btw_30189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7btw_30189/03_2026/7btw_30189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7btw_30189/03_2026/7btw_30189.map" model { file = "/net/cci-nas-00/data/ceres_data/7btw_30189/03_2026/7btw_30189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7btw_30189/03_2026/7btw_30189.cif" } resolution = 2.9 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= 0.020 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 45 5.16 5 C 6552 2.51 5 N 1747 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10246 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2775 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2410 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain breaks: 2 Chain: "C" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2286 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 6, 'TRANS': 277} Chain breaks: 2 Chain: "D" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2775 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.47, per 1000 atoms: 0.24 Number of scatterers: 10246 At special positions: 0 Unit cell: (104.58, 103.335, 103.335, 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 45 16.00 O 1902 8.00 N 1747 7.00 C 6552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 472.9 milliseconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 31.3% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 263 through 270 removed outlier: 3.639A pdb=" N SER A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.537A pdb=" N GLN A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 37 removed outlier: 3.580A pdb=" N GLU B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 157 through 181 removed outlier: 3.716A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 193 removed outlier: 3.537A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.658A pdb=" N GLN B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.615A pdb=" N LEU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 234 through 243 removed outlier: 3.794A pdb=" N GLY B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 273 removed outlier: 3.632A pdb=" N SER B 251 " --> pdb=" O ASN B 247 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 252 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 297 removed outlier: 3.588A pdb=" N TYR B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 312 Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 324 through 327 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.611A pdb=" N SER C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.729A pdb=" N LEU C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 121 through 132 removed outlier: 3.914A pdb=" N LEU C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.545A pdb=" N TYR C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.506A pdb=" N LEU C 149 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 154 removed outlier: 3.787A pdb=" N TRP C 154 " --> pdb=" O PHE C 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 155 through 169 removed outlier: 3.630A pdb=" N GLN C 160 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 161 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 244 removed outlier: 3.584A pdb=" N GLU C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 263 removed outlier: 3.599A pdb=" N LEU C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 296 removed outlier: 4.039A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N SER C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N GLU C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 291 " --> pdb=" O MET C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 removed outlier: 4.439A pdb=" N ASN C 321 " --> pdb=" O MET C 317 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 270 removed outlier: 3.639A pdb=" N SER D 268 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 270 " --> pdb=" O MET D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 434 removed outlier: 3.536A pdb=" N GLN D 433 " --> pdb=" O ASN D 429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.692A pdb=" N GLY A 128 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER A 171 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 168 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN A 196 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 416 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR A 440 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 442 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.692A pdb=" N GLY A 128 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER A 171 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 168 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN A 196 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 416 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR A 440 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 442 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 21 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.733A pdb=" N ILE B 130 " --> pdb=" O GLY B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA5, first strand: chain 'C' and resid 44 through 47 removed outlier: 7.038A pdb=" N GLY C 4 " --> pdb=" O GLN C 45 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL C 47 " --> pdb=" O GLY C 4 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL C 6 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 126 through 127 removed outlier: 4.069A pdb=" N SER D 171 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE D 168 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN D 196 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 416 " --> pdb=" O TYR D 390 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR D 440 " --> pdb=" O ILE D 463 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 442 " --> pdb=" O LEU D 461 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1863 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: 1.74 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 9 1.18 - 1.34: 3201 1.34 - 1.50: 2926 1.50 - 1.65: 4261 1.65 - 1.81: 67 Bond restraints: 10464 Sorted by residual: bond pdb=" C ARG D 164 " pdb=" O ARG D 164 " ideal model delta sigma weight residual 1.234 1.023 0.211 1.28e-02 6.10e+03 2.72e+02 bond pdb=" CA ASN A 135 " pdb=" C ASN A 135 " ideal model delta sigma weight residual 1.522 1.309 0.212 1.33e-02 5.65e+03 2.55e+02 bond pdb=" C ARG A 164 " pdb=" O ARG A 164 " ideal model delta sigma weight residual 1.234 1.106 0.128 1.11e-02 8.12e+03 1.33e+02 bond pdb=" C ASN A 135 " pdb=" O ASN A 135 " ideal model delta sigma weight residual 1.238 1.032 0.206 1.83e-02 2.99e+03 1.27e+02 bond pdb=" C ASN A 133 " pdb=" O ASN A 133 " ideal model delta sigma weight residual 1.236 1.148 0.089 1.16e-02 7.43e+03 5.88e+01 ... (remaining 10459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 13909 3.54 - 7.08: 173 7.08 - 10.62: 33 10.62 - 14.17: 7 14.17 - 17.71: 8 Bond angle restraints: 14130 Sorted by residual: angle pdb=" N ASN A 135 " pdb=" CA ASN A 135 " pdb=" C ASN A 135 " ideal model delta sigma weight residual 113.56 95.85 17.71 1.39e+00 5.18e-01 1.62e+02 angle pdb=" O LEU D 163 " pdb=" C LEU D 163 " pdb=" N ARG D 164 " ideal model delta sigma weight residual 123.29 110.02 13.27 1.18e+00 7.18e-01 1.27e+02 angle pdb=" CA LEU D 163 " pdb=" C LEU D 163 " pdb=" N ARG D 164 " ideal model delta sigma weight residual 116.28 127.17 -10.89 1.26e+00 6.30e-01 7.47e+01 angle pdb=" C ALA D 139 " pdb=" N TYR D 140 " pdb=" CA TYR D 140 " ideal model delta sigma weight residual 122.81 108.60 14.21 1.68e+00 3.54e-01 7.15e+01 angle pdb=" C ARG D 164 " pdb=" N GLY D 165 " pdb=" CA GLY D 165 " ideal model delta sigma weight residual 120.84 136.37 -15.53 1.91e+00 2.74e-01 6.61e+01 ... (remaining 14125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 5301 17.14 - 34.29: 638 34.29 - 51.43: 200 51.43 - 68.57: 81 68.57 - 85.72: 14 Dihedral angle restraints: 6234 sinusoidal: 2526 harmonic: 3708 Sorted by residual: dihedral pdb=" CA LEU C 60 " pdb=" C LEU C 60 " pdb=" N PRO C 61 " pdb=" CA PRO C 61 " ideal model delta harmonic sigma weight residual 180.00 129.36 50.64 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" N ASN A 133 " pdb=" C ASN A 133 " pdb=" CA ASN A 133 " pdb=" CB ASN A 133 " ideal model delta harmonic sigma weight residual 122.80 142.10 -19.30 0 2.50e+00 1.60e-01 5.96e+01 dihedral pdb=" CA THR D 199 " pdb=" C THR D 199 " pdb=" N ASN D 200 " pdb=" CA ASN D 200 " ideal model delta harmonic sigma weight residual 180.00 142.03 37.97 0 5.00e+00 4.00e-02 5.77e+01 ... (remaining 6231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 1542 0.149 - 0.298: 27 0.298 - 0.447: 3 0.447 - 0.596: 0 0.596 - 0.745: 2 Chirality restraints: 1574 Sorted by residual: chirality pdb=" CA THR C 87 " pdb=" N THR C 87 " pdb=" C THR C 87 " pdb=" CB THR C 87 " both_signs ideal model delta sigma weight residual False 2.53 1.78 0.74 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CA ASN A 133 " pdb=" N ASN A 133 " pdb=" C ASN A 133 " pdb=" CB ASN A 133 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA LEU B 128 " pdb=" N LEU B 128 " pdb=" C LEU B 128 " pdb=" CB LEU B 128 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 1571 not shown) Planarity restraints: 1790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 135 " 0.029 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C ASN A 135 " -0.095 2.00e-02 2.50e+03 pdb=" O ASN A 135 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP A 136 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 163 " 0.026 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" C LEU D 163 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU D 163 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG D 164 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 60 " -0.074 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO C 61 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.059 5.00e-02 4.00e+02 ... (remaining 1787 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.22: 1 2.22 - 2.89: 3711 2.89 - 3.56: 13062 3.56 - 4.23: 24478 4.23 - 4.90: 42307 Nonbonded interactions: 83559 Sorted by model distance: nonbonded pdb=" O THR D 129 " pdb=" O ALA D 137 " model vdw 1.556 3.040 nonbonded pdb=" ND2 ASN D 130 " pdb=" O GLU D 138 " model vdw 2.231 3.120 nonbonded pdb=" N ASN A 135 " pdb=" N ASP A 136 " model vdw 2.232 2.560 nonbonded pdb=" OG SER B 184 " pdb=" OE2 GLU B 301 " model vdw 2.278 3.040 nonbonded pdb=" OG SER A 344 " pdb=" O SER A 348 " model vdw 2.279 3.040 ... (remaining 83554 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' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.910 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 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 : 0.008 0.212 10464 Z= 0.447 Angle : 1.122 17.707 14130 Z= 0.625 Chirality : 0.063 0.745 1574 Planarity : 0.008 0.111 1790 Dihedral : 18.114 85.718 3840 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.02 % Favored : 91.59 % Rotamer: Outliers : 9.60 % Allowed : 7.59 % Favored : 82.81 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.49 % 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 are not related in a simple way. whole: -5.22 (0.18), residues: 1260 helix: -4.29 (0.11), residues: 360 sheet: -2.41 (0.24), residues: 384 loop : -3.49 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 39 TYR 0.024 0.003 TYR C 137 PHE 0.064 0.003 PHE A 331 TRP 0.017 0.002 TRP D 301 HIS 0.008 0.002 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00793 (10464) covalent geometry : angle 1.12170 (14130) hydrogen bonds : bond 0.27278 ( 519) hydrogen bonds : angle 10.68290 ( 1863) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 186 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.4619 (OUTLIER) cc_final: 0.4411 (mmmt) REVERT: A 170 SER cc_start: 0.8131 (p) cc_final: 0.7906 (t) REVERT: A 291 MET cc_start: 0.5037 (ttp) cc_final: 0.3673 (tmm) REVERT: A 405 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.5806 (pptt) REVERT: A 409 ARG cc_start: 0.7815 (mmt90) cc_final: 0.7514 (mmm-85) REVERT: A 457 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7120 (tm) REVERT: B 162 MET cc_start: 0.8046 (mmp) cc_final: 0.7174 (mmp) REVERT: B 168 ASP cc_start: 0.8259 (m-30) cc_final: 0.8052 (m-30) REVERT: B 185 ASP cc_start: 0.7820 (m-30) cc_final: 0.7488 (m-30) REVERT: B 189 MET cc_start: 0.8433 (mmm) cc_final: 0.8106 (mmm) REVERT: C 21 ASP cc_start: 0.7056 (m-30) cc_final: 0.6768 (m-30) REVERT: D 154 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5312 (pp) REVERT: D 164 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5487 (mtm-85) REVERT: D 193 GLN cc_start: 0.7427 (pt0) cc_final: 0.7226 (pt0) REVERT: D 442 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7788 (t) outliers start: 110 outliers final: 13 residues processed: 276 average time/residue: 0.5705 time to fit residues: 169.1828 Evaluate side-chains 137 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 254 GLN Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 442 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.0070 chunk 51 optimal weight: 0.0000 overall best weight: 0.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN A 476 GLN B 26 GLN B 72 ASN B 94 ASN B 234 HIS B 256 GLN B 321 GLN C 7 HIS C 116 ASN C 138 ASN C 222 ASN C 269 ASN D 200 ASN D 254 GLN D 273 GLN D 422 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.188016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.156138 restraints weight = 10410.170| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.70 r_work: 0.3620 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10464 Z= 0.125 Angle : 0.659 9.589 14130 Z= 0.354 Chirality : 0.043 0.215 1574 Planarity : 0.006 0.078 1790 Dihedral : 8.360 59.334 1405 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.40 % Allowed : 16.32 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.32 % 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 are not related in a simple way. whole: -3.65 (0.20), residues: 1260 helix: -1.78 (0.22), residues: 373 sheet: -1.83 (0.24), residues: 363 loop : -3.27 (0.22), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 409 TYR 0.016 0.001 TYR B 164 PHE 0.017 0.001 PHE B 18 TRP 0.023 0.002 TRP A 323 HIS 0.005 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00261 (10464) covalent geometry : angle 0.65892 (14130) hydrogen bonds : bond 0.03789 ( 519) hydrogen bonds : angle 5.33692 ( 1863) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.413 Fit side-chains REVERT: A 291 MET cc_start: 0.5487 (ttp) cc_final: 0.3498 (tmm) REVERT: A 295 LYS cc_start: 0.8089 (tppt) cc_final: 0.7082 (ttpt) REVERT: A 316 GLU cc_start: 0.8273 (tt0) cc_final: 0.8039 (tt0) REVERT: B 189 MET cc_start: 0.8644 (mmm) cc_final: 0.8357 (mmm) REVERT: B 263 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7461 (mm-30) REVERT: B 275 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7152 (ptt) REVERT: C 14 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: C 21 ASP cc_start: 0.7437 (m-30) cc_final: 0.7182 (m-30) REVERT: C 168 ASN cc_start: 0.7531 (t0) cc_final: 0.7270 (t0) REVERT: D 136 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: D 195 TYR cc_start: 0.7192 (p90) cc_final: 0.6895 (p90) REVERT: D 261 MET cc_start: 0.1483 (ttm) cc_final: 0.1244 (mtp) REVERT: D 291 MET cc_start: 0.5235 (tmt) cc_final: 0.4613 (pmm) outliers start: 39 outliers final: 16 residues processed: 162 average time/residue: 0.5551 time to fit residues: 97.0897 Evaluate side-chains 114 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 441 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS B 26 GLN C 82 HIS C 84 ASN C 129 GLN C 300 ASN D 133 ASN D 273 GLN D 280 HIS D 369 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.181908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149721 restraints weight = 10391.775| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.92 r_work: 0.3508 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10464 Z= 0.147 Angle : 0.632 9.691 14130 Z= 0.339 Chirality : 0.044 0.246 1574 Planarity : 0.005 0.089 1790 Dihedral : 6.664 48.378 1375 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.38 % Favored : 92.54 % Rotamer: Outliers : 4.36 % Allowed : 18.94 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.24 % 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 are not related in a simple way. whole: -2.61 (0.22), residues: 1260 helix: -0.26 (0.26), residues: 377 sheet: -1.54 (0.24), residues: 387 loop : -3.03 (0.23), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 409 TYR 0.014 0.001 TYR C 137 PHE 0.019 0.002 PHE A 331 TRP 0.022 0.002 TRP A 323 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00321 (10464) covalent geometry : angle 0.63177 (14130) hydrogen bonds : bond 0.03421 ( 519) hydrogen bonds : angle 4.73951 ( 1863) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 117 time to evaluate : 0.440 Fit side-chains REVERT: A 291 MET cc_start: 0.5426 (ttp) cc_final: 0.4373 (tmt) REVERT: A 295 LYS cc_start: 0.8391 (tppt) cc_final: 0.7363 (ttpt) REVERT: A 316 GLU cc_start: 0.8334 (tt0) cc_final: 0.8041 (tt0) REVERT: A 436 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7600 (ptpp) REVERT: A 452 MET cc_start: 0.6634 (mtm) cc_final: 0.5995 (mmm) REVERT: A 467 GLU cc_start: 0.6961 (tp30) cc_final: 0.6713 (tp30) REVERT: B 73 THR cc_start: 0.8347 (t) cc_final: 0.8066 (p) REVERT: B 239 LYS cc_start: 0.8471 (ttmt) cc_final: 0.7503 (tttt) REVERT: B 291 SER cc_start: 0.9277 (p) cc_final: 0.9072 (m) REVERT: C 21 ASP cc_start: 0.7613 (m-30) cc_final: 0.7190 (m-30) REVERT: C 168 ASN cc_start: 0.7713 (t0) cc_final: 0.7414 (t0) REVERT: C 248 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7780 (pt) REVERT: D 195 TYR cc_start: 0.7453 (p90) cc_final: 0.7204 (p90) REVERT: D 261 MET cc_start: 0.1465 (ttm) cc_final: 0.1262 (mtt) outliers start: 50 outliers final: 16 residues processed: 155 average time/residue: 0.5540 time to fit residues: 92.7022 Evaluate side-chains 115 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 337 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN A 347 GLN A 476 GLN B 234 HIS B 249 HIS C 50 ASN C 116 ASN C 269 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.174672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.141762 restraints weight = 10577.116| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.02 r_work: 0.3414 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10464 Z= 0.227 Angle : 0.714 10.253 14130 Z= 0.380 Chirality : 0.047 0.277 1574 Planarity : 0.006 0.091 1790 Dihedral : 6.674 49.288 1370 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.90 % Rotamer: Outliers : 4.45 % Allowed : 20.59 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.16 % 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 are not related in a simple way. whole: -2.41 (0.22), residues: 1260 helix: 0.10 (0.27), residues: 372 sheet: -1.26 (0.25), residues: 351 loop : -3.11 (0.22), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 376 TYR 0.020 0.002 TYR C 137 PHE 0.022 0.002 PHE A 331 TRP 0.011 0.002 TRP D 412 HIS 0.006 0.002 HIS D 352 Details of bonding type rmsd covalent geometry : bond 0.00529 (10464) covalent geometry : angle 0.71361 (14130) hydrogen bonds : bond 0.03703 ( 519) hydrogen bonds : angle 4.94936 ( 1863) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 0.391 Fit side-chains REVERT: A 295 LYS cc_start: 0.8380 (tppt) cc_final: 0.8080 (mptp) REVERT: A 316 GLU cc_start: 0.8514 (tt0) cc_final: 0.8254 (tt0) REVERT: A 392 LEU cc_start: 0.8877 (tt) cc_final: 0.8667 (tp) REVERT: A 437 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6749 (mt-10) REVERT: A 452 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6283 (mmm) REVERT: A 461 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8362 (mt) REVERT: A 472 ARG cc_start: 0.7074 (ttm-80) cc_final: 0.6795 (ttt-90) REVERT: B 73 THR cc_start: 0.8629 (t) cc_final: 0.8264 (p) REVERT: B 155 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7538 (mp) REVERT: B 168 ASP cc_start: 0.8631 (m-30) cc_final: 0.8427 (m-30) REVERT: B 291 SER cc_start: 0.9347 (p) cc_final: 0.9080 (m) REVERT: B 312 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7200 (mt-10) REVERT: C 3 LYS cc_start: 0.7932 (mptm) cc_final: 0.7484 (tppt) REVERT: D 215 ARG cc_start: 0.7826 (ttt180) cc_final: 0.7417 (mtp180) REVERT: D 261 MET cc_start: 0.1910 (ttm) cc_final: 0.1281 (mtt) REVERT: D 266 MET cc_start: 0.7024 (mtt) cc_final: 0.6700 (mtt) outliers start: 51 outliers final: 25 residues processed: 158 average time/residue: 0.5481 time to fit residues: 93.4228 Evaluate side-chains 127 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 441 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 105 optimal weight: 10.0000 chunk 87 optimal weight: 0.0570 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 43 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN ** D 450 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 = 0.3998 r_free = 0.3998 target = 0.178220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144777 restraints weight = 10432.674| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.97 r_work: 0.3458 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10464 Z= 0.129 Angle : 0.605 8.758 14130 Z= 0.325 Chirality : 0.043 0.221 1574 Planarity : 0.005 0.082 1790 Dihedral : 6.150 43.350 1370 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.01 % Allowed : 21.47 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -1.97 (0.22), residues: 1260 helix: 0.58 (0.27), residues: 378 sheet: -1.12 (0.24), residues: 372 loop : -2.95 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 275 TYR 0.015 0.001 TYR C 137 PHE 0.016 0.001 PHE A 237 TRP 0.014 0.001 TRP A 301 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00289 (10464) covalent geometry : angle 0.60518 (14130) hydrogen bonds : bond 0.03056 ( 519) hydrogen bonds : angle 4.48655 ( 1863) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.399 Fit side-chains REVERT: A 295 LYS cc_start: 0.8374 (tppt) cc_final: 0.8033 (mptp) REVERT: A 316 GLU cc_start: 0.8312 (tt0) cc_final: 0.7970 (tt0) REVERT: A 436 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7558 (ptpp) REVERT: A 437 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6609 (tt0) REVERT: A 452 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6436 (mmm) REVERT: B 73 THR cc_start: 0.8529 (t) cc_final: 0.8236 (p) REVERT: B 291 SER cc_start: 0.9274 (p) cc_final: 0.9046 (m) REVERT: C 21 ASP cc_start: 0.7633 (m-30) cc_final: 0.7208 (m-30) REVERT: D 215 ARG cc_start: 0.7830 (ttt180) cc_final: 0.7463 (mtp180) REVERT: D 261 MET cc_start: 0.1733 (ttm) cc_final: 0.1211 (mtt) REVERT: D 266 MET cc_start: 0.7038 (mtt) cc_final: 0.6692 (mtt) outliers start: 46 outliers final: 20 residues processed: 148 average time/residue: 0.5294 time to fit residues: 84.4090 Evaluate side-chains 129 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 441 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 90 optimal weight: 0.0980 chunk 93 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 450 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 = 0.3942 r_free = 0.3942 target = 0.172974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.139757 restraints weight = 10495.150| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.07 r_work: 0.3444 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10464 Z= 0.229 Angle : 0.712 10.020 14130 Z= 0.377 Chirality : 0.047 0.271 1574 Planarity : 0.005 0.090 1790 Dihedral : 6.503 45.659 1370 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.89 % Favored : 91.03 % Rotamer: Outliers : 5.06 % Allowed : 21.29 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.16 % 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 are not related in a simple way. whole: -2.03 (0.22), residues: 1260 helix: 0.44 (0.27), residues: 379 sheet: -1.28 (0.25), residues: 370 loop : -2.79 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 153 TYR 0.018 0.002 TYR C 137 PHE 0.014 0.002 PHE D 237 TRP 0.023 0.002 TRP A 323 HIS 0.006 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00538 (10464) covalent geometry : angle 0.71153 (14130) hydrogen bonds : bond 0.03583 ( 519) hydrogen bonds : angle 4.82733 ( 1863) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 107 time to evaluate : 0.380 Fit side-chains REVERT: A 291 MET cc_start: 0.4260 (OUTLIER) cc_final: 0.3270 (ttp) REVERT: A 295 LYS cc_start: 0.8420 (tppt) cc_final: 0.8140 (mptp) REVERT: A 321 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8048 (ttpt) REVERT: A 437 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: A 452 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.6977 (mmm) REVERT: B 73 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8152 (p) REVERT: B 263 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: B 291 SER cc_start: 0.9335 (p) cc_final: 0.9109 (m) REVERT: C 3 LYS cc_start: 0.7997 (mptm) cc_final: 0.7562 (tppt) REVERT: C 102 ILE cc_start: 0.7933 (mm) cc_final: 0.7663 (mp) REVERT: C 105 LYS cc_start: 0.7756 (ttmt) cc_final: 0.7482 (tttm) REVERT: C 111 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: D 215 ARG cc_start: 0.7832 (ttt180) cc_final: 0.7525 (mtp180) REVERT: D 261 MET cc_start: 0.1633 (ttm) cc_final: 0.1007 (mtt) REVERT: D 266 MET cc_start: 0.7025 (mtt) cc_final: 0.6647 (mtt) outliers start: 58 outliers final: 27 residues processed: 154 average time/residue: 0.5997 time to fit residues: 98.9328 Evaluate side-chains 134 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 441 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 123 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN ** D 450 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 = 0.4128 r_free = 0.4128 target = 0.188531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.158691 restraints weight = 10220.383| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.67 r_work: 0.3612 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10464 Z= 0.132 Angle : 0.610 8.594 14130 Z= 0.326 Chirality : 0.043 0.220 1574 Planarity : 0.005 0.081 1790 Dihedral : 6.086 40.195 1370 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.40 % Allowed : 23.56 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -1.79 (0.23), residues: 1260 helix: 0.86 (0.27), residues: 379 sheet: -1.28 (0.25), residues: 368 loop : -2.72 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 472 TYR 0.016 0.001 TYR C 137 PHE 0.018 0.001 PHE A 237 TRP 0.014 0.002 TRP A 301 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00297 (10464) covalent geometry : angle 0.60959 (14130) hydrogen bonds : bond 0.03020 ( 519) hydrogen bonds : angle 4.45764 ( 1863) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 0.291 Fit side-chains REVERT: A 295 LYS cc_start: 0.8328 (tppt) cc_final: 0.7637 (ttpt) REVERT: A 321 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7730 (ttpt) REVERT: A 437 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6801 (tt0) REVERT: A 452 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6752 (mmm) REVERT: B 73 THR cc_start: 0.8558 (t) cc_final: 0.8282 (p) REVERT: B 291 SER cc_start: 0.9215 (p) cc_final: 0.8993 (m) REVERT: C 3 LYS cc_start: 0.7772 (mptm) cc_final: 0.7454 (tppt) REVERT: C 102 ILE cc_start: 0.7824 (mm) cc_final: 0.7524 (mp) REVERT: D 261 MET cc_start: 0.1518 (ttm) cc_final: 0.1216 (mtt) REVERT: D 266 MET cc_start: 0.7158 (mtt) cc_final: 0.6687 (mtt) outliers start: 39 outliers final: 20 residues processed: 136 average time/residue: 0.5338 time to fit residues: 78.4385 Evaluate side-chains 124 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 441 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 92 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN B 242 GLN D 130 ASN D 450 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.168516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135768 restraints weight = 10646.683| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.03 r_work: 0.3350 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 10464 Z= 0.379 Angle : 0.851 11.155 14130 Z= 0.448 Chirality : 0.054 0.325 1574 Planarity : 0.006 0.095 1790 Dihedral : 6.777 45.535 1366 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.73 % Favored : 91.11 % Rotamer: Outliers : 4.54 % Allowed : 23.04 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.24 % 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 are not related in a simple way. whole: -2.18 (0.22), residues: 1260 helix: 0.24 (0.26), residues: 375 sheet: -1.25 (0.24), residues: 376 loop : -2.89 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 275 TYR 0.050 0.003 TYR C 137 PHE 0.020 0.003 PHE A 194 TRP 0.013 0.003 TRP D 412 HIS 0.011 0.003 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00893 (10464) covalent geometry : angle 0.85099 (14130) hydrogen bonds : bond 0.04215 ( 519) hydrogen bonds : angle 5.20922 ( 1863) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 103 time to evaluate : 0.398 Fit side-chains REVERT: A 295 LYS cc_start: 0.8385 (tppt) cc_final: 0.8064 (mptp) REVERT: A 321 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8142 (ttpt) REVERT: A 437 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: A 452 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6547 (mmm) REVERT: B 73 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8001 (p) REVERT: B 291 SER cc_start: 0.9392 (p) cc_final: 0.9110 (m) REVERT: B 312 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: C 111 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: C 310 ARG cc_start: 0.6624 (mmt90) cc_final: 0.6422 (mmt90) REVERT: D 261 MET cc_start: 0.1877 (ttm) cc_final: 0.1234 (mtt) REVERT: D 266 MET cc_start: 0.7056 (mtt) cc_final: 0.6591 (mtt) outliers start: 52 outliers final: 30 residues processed: 139 average time/residue: 0.5631 time to fit residues: 84.5733 Evaluate side-chains 132 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 470 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN B 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.175978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143689 restraints weight = 10407.835| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.90 r_work: 0.3506 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10464 Z= 0.140 Angle : 0.626 8.761 14130 Z= 0.335 Chirality : 0.044 0.224 1574 Planarity : 0.005 0.081 1790 Dihedral : 6.046 35.365 1366 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.23 % Allowed : 24.96 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -1.73 (0.23), residues: 1260 helix: 0.93 (0.27), residues: 374 sheet: -1.13 (0.26), residues: 338 loop : -2.70 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 275 TYR 0.026 0.002 TYR C 137 PHE 0.019 0.001 PHE A 237 TRP 0.024 0.002 TRP A 301 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00314 (10464) covalent geometry : angle 0.62605 (14130) hydrogen bonds : bond 0.03110 ( 519) hydrogen bonds : angle 4.53449 ( 1863) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.335 Fit side-chains REVERT: A 295 LYS cc_start: 0.8295 (tppt) cc_final: 0.7506 (ttpt) REVERT: A 321 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7871 (ttpt) REVERT: A 437 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6897 (tt0) REVERT: B 73 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8181 (p) REVERT: B 263 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7519 (mm-30) REVERT: B 291 SER cc_start: 0.9216 (p) cc_final: 0.9001 (m) REVERT: C 3 LYS cc_start: 0.7879 (mptm) cc_final: 0.7515 (tppt) REVERT: C 21 ASP cc_start: 0.7474 (m-30) cc_final: 0.6986 (m-30) REVERT: C 102 ILE cc_start: 0.7769 (mm) cc_final: 0.7528 (mp) REVERT: D 154 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6193 (pp) REVERT: D 266 MET cc_start: 0.7257 (mtt) cc_final: 0.6866 (mtt) REVERT: D 402 LYS cc_start: 0.6351 (tttt) cc_final: 0.5984 (tmtt) outliers start: 37 outliers final: 19 residues processed: 125 average time/residue: 0.5624 time to fit residues: 76.0872 Evaluate side-chains 117 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 441 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 GLN B 242 GLN C 133 ASN D 130 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.177417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.146270 restraints weight = 10350.557| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.93 r_work: 0.3615 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10464 Z= 0.126 Angle : 0.613 8.986 14130 Z= 0.326 Chirality : 0.043 0.211 1574 Planarity : 0.005 0.089 1790 Dihedral : 5.778 36.447 1366 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.79 % Allowed : 26.35 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -1.54 (0.23), residues: 1260 helix: 1.23 (0.28), residues: 368 sheet: -1.04 (0.26), residues: 340 loop : -2.64 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 275 TYR 0.020 0.001 TYR C 137 PHE 0.018 0.001 PHE A 237 TRP 0.021 0.002 TRP A 301 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00285 (10464) covalent geometry : angle 0.61261 (14130) hydrogen bonds : bond 0.02951 ( 519) hydrogen bonds : angle 4.33935 ( 1863) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.386 Fit side-chains REVERT: A 159 ASN cc_start: 0.7353 (m-40) cc_final: 0.7145 (m-40) REVERT: A 291 MET cc_start: 0.4120 (OUTLIER) cc_final: 0.3856 (mmm) REVERT: A 295 LYS cc_start: 0.8203 (tppt) cc_final: 0.7407 (ttpt) REVERT: A 321 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7548 (ttpt) REVERT: A 324 MET cc_start: 0.7046 (mmm) cc_final: 0.6750 (mtt) REVERT: A 437 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: B 73 THR cc_start: 0.8540 (t) cc_final: 0.8184 (p) REVERT: B 162 MET cc_start: 0.8123 (mmt) cc_final: 0.7576 (mmp) REVERT: B 263 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: C 3 LYS cc_start: 0.7656 (mptm) cc_final: 0.7242 (tppt) REVERT: C 21 ASP cc_start: 0.7607 (m-30) cc_final: 0.7136 (m-30) REVERT: C 102 ILE cc_start: 0.7687 (mm) cc_final: 0.7401 (mp) REVERT: D 154 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6428 (pp) REVERT: D 266 MET cc_start: 0.7000 (mtt) cc_final: 0.6583 (mtt) REVERT: D 402 LYS cc_start: 0.6719 (tttt) cc_final: 0.6249 (tmtt) REVERT: D 459 PHE cc_start: 0.8187 (t80) cc_final: 0.7596 (t80) outliers start: 32 outliers final: 14 residues processed: 132 average time/residue: 0.5375 time to fit residues: 76.8750 Evaluate side-chains 123 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 441 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 107 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.8744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN D 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.177117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.145112 restraints weight = 10468.177| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.02 r_work: 0.3610 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10464 Z= 0.132 Angle : 0.614 8.753 14130 Z= 0.325 Chirality : 0.043 0.217 1574 Planarity : 0.005 0.084 1790 Dihedral : 5.722 36.611 1366 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.44 % Allowed : 26.79 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -1.42 (0.23), residues: 1260 helix: 1.36 (0.28), residues: 368 sheet: -0.99 (0.26), residues: 340 loop : -2.59 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 275 TYR 0.018 0.001 TYR C 137 PHE 0.017 0.001 PHE A 237 TRP 0.020 0.002 TRP A 301 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00302 (10464) covalent geometry : angle 0.61351 (14130) hydrogen bonds : bond 0.02966 ( 519) hydrogen bonds : angle 4.31431 ( 1863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3597.88 seconds wall clock time: 62 minutes 6.11 seconds (3726.11 seconds total)