Starting phenix.real_space_refine on Mon Jul 28 05:49:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7btw_30189/07_2025/7btw_30189.cif Found real_map, /net/cci-nas-00/data/ceres_data/7btw_30189/07_2025/7btw_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_30189/07_2025/7btw_30189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7btw_30189/07_2025/7btw_30189.map" model { file = "/net/cci-nas-00/data/ceres_data/7btw_30189/07_2025/7btw_30189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7btw_30189/07_2025/7btw_30189.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.41, per 1000 atoms: 0.63 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.08 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: 3.48 Time building geometry restraints manager: 2.78 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: 0.450 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.020 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:14.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.002 TRP D 301 HIS 0.008 0.002 HIS A 310 PHE 0.064 0.003 PHE A 331 TYR 0.024 0.003 TYR C 137 ARG 0.005 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.27278 ( 519) hydrogen bonds : angle 10.68290 ( 1863) covalent geometry : bond 0.00793 (10464) covalent geometry : angle 1.12170 (14130) *********************** 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 : 1.158 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: 0.7512 (mmm-85) REVERT: A 457 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7122 (tm) REVERT: B 151 ARG cc_start: 0.8090 (ttm110) cc_final: 0.7890 (ttp-170) 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: 1.1103 time to fit residues: 330.5166 Evaluate side-chains 138 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 106 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.0870 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 422 HIS B 72 ASN B 94 ASN B 256 GLN B 321 GLN C 7 HIS C 82 HIS C 138 ASN C 222 ASN C 269 ASN D 200 ASN D 254 GLN D 273 GLN D 280 HIS D 303 ASN D 422 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.176768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.143095 restraints weight = 10413.704| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.92 r_work: 0.3454 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10464 Z= 0.213 Angle : 0.753 10.542 14130 Z= 0.403 Chirality : 0.047 0.281 1574 Planarity : 0.007 0.095 1790 Dihedral : 8.543 56.609 1405 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.54 % Favored : 92.38 % Rotamer: Outliers : 3.93 % Allowed : 17.63 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.20), residues: 1260 helix: -1.84 (0.21), residues: 370 sheet: -1.88 (0.24), residues: 363 loop : -3.28 (0.22), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 323 HIS 0.007 0.001 HIS B 234 PHE 0.021 0.002 PHE B 18 TYR 0.021 0.002 TYR C 137 ARG 0.005 0.001 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 519) hydrogen bonds : angle 5.53814 ( 1863) covalent geometry : bond 0.00484 (10464) covalent geometry : angle 0.75256 (14130) *********************** 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 177 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 1.053 Fit side-chains REVERT: A 291 MET cc_start: 0.5531 (ttp) cc_final: 0.4417 (tmt) REVERT: A 295 LYS cc_start: 0.8412 (tppt) cc_final: 0.7420 (ttpt) REVERT: A 316 GLU cc_start: 0.8456 (tt0) cc_final: 0.8170 (tt0) REVERT: A 321 LYS cc_start: 0.8187 (tttt) cc_final: 0.7769 (ttpp) REVERT: A 323 TRP cc_start: 0.7510 (m-90) cc_final: 0.7285 (m-90) REVERT: A 409 ARG cc_start: 0.7795 (mmt90) cc_final: 0.7551 (mmm-85) REVERT: A 437 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.5405 (mp0) REVERT: A 452 MET cc_start: 0.6478 (OUTLIER) cc_final: 0.5828 (mmm) REVERT: A 457 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7608 (tm) REVERT: B 73 THR cc_start: 0.8382 (t) cc_final: 0.7946 (p) REVERT: B 151 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7914 (ttp-110) REVERT: B 196 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6322 (mmtt) REVERT: B 263 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7554 (mm-30) REVERT: C 3 LYS cc_start: 0.7937 (mptm) cc_final: 0.7529 (tppt) REVERT: C 14 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: C 21 ASP cc_start: 0.7684 (m-30) cc_final: 0.7234 (m-30) REVERT: C 168 ASN cc_start: 0.7900 (t0) cc_final: 0.7561 (t0) REVERT: D 136 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7738 (m-30) REVERT: D 442 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8531 (t) outliers start: 45 outliers final: 20 residues processed: 164 average time/residue: 1.1376 time to fit residues: 202.1311 Evaluate side-chains 131 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 208 ARG 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 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 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER 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 Chi-restraints excluded: chain D residue 442 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 103 optimal weight: 0.0570 chunk 95 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 HIS A 458 ASN B 72 ASN C 84 ASN C 300 ASN C 314 ASN D 273 GLN D 303 ASN D 369 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.182855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151195 restraints weight = 10417.312| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.87 r_work: 0.3533 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 10464 Z= 0.112 Angle : 0.595 8.652 14130 Z= 0.322 Chirality : 0.042 0.208 1574 Planarity : 0.005 0.080 1790 Dihedral : 6.899 55.677 1378 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.66 % Allowed : 20.33 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.21), residues: 1260 helix: -0.26 (0.26), residues: 377 sheet: -1.30 (0.26), residues: 345 loop : -3.12 (0.22), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 301 HIS 0.004 0.001 HIS B 234 PHE 0.016 0.001 PHE A 331 TYR 0.014 0.001 TYR C 137 ARG 0.005 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 519) hydrogen bonds : angle 4.71210 ( 1863) covalent geometry : bond 0.00241 (10464) covalent geometry : angle 0.59533 (14130) *********************** 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 170 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 1.060 Fit side-chains REVERT: A 198 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7374 (m-40) REVERT: A 291 MET cc_start: 0.5419 (ttp) cc_final: 0.4350 (tmt) REVERT: A 295 LYS cc_start: 0.8345 (tppt) cc_final: 0.7358 (ttpt) REVERT: A 316 GLU cc_start: 0.8263 (tt0) cc_final: 0.7971 (tt0) REVERT: A 409 ARG cc_start: 0.7726 (mmt90) cc_final: 0.7449 (mmm-85) REVERT: A 452 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.5908 (mmm) REVERT: A 457 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7323 (tm) REVERT: A 461 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8380 (mt) REVERT: B 73 THR cc_start: 0.8397 (t) cc_final: 0.8103 (p) REVERT: B 151 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7837 (ttp-110) REVERT: B 162 MET cc_start: 0.7981 (mmt) cc_final: 0.7619 (mmp) REVERT: C 14 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: C 21 ASP cc_start: 0.7489 (m-30) cc_final: 0.6974 (m-30) REVERT: C 168 ASN cc_start: 0.7647 (t0) cc_final: 0.7373 (t0) REVERT: D 266 MET cc_start: 0.6661 (mtt) cc_final: 0.6408 (mtt) REVERT: D 371 PHE cc_start: 0.7893 (m-10) cc_final: 0.7662 (m-10) REVERT: D 442 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8458 (t) outliers start: 42 outliers final: 12 residues processed: 162 average time/residue: 1.1261 time to fit residues: 197.4551 Evaluate side-chains 122 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER 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 45 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 442 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 64 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 249 HIS C 50 ASN C 129 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.174394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142902 restraints weight = 10496.400| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.91 r_work: 0.3419 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10464 Z= 0.217 Angle : 0.704 10.428 14130 Z= 0.376 Chirality : 0.046 0.273 1574 Planarity : 0.006 0.093 1790 Dihedral : 6.895 55.293 1374 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.90 % Rotamer: Outliers : 4.71 % Allowed : 20.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.22), residues: 1260 helix: 0.08 (0.27), residues: 377 sheet: -1.30 (0.25), residues: 370 loop : -3.09 (0.23), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 323 HIS 0.005 0.001 HIS B 234 PHE 0.020 0.002 PHE D 331 TYR 0.020 0.002 TYR C 137 ARG 0.007 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 519) hydrogen bonds : angle 4.92032 ( 1863) covalent geometry : bond 0.00498 (10464) covalent geometry : angle 0.70422 (14130) *********************** 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: 54 poor density : 113 time to evaluate : 1.120 Fit side-chains REVERT: A 198 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7734 (m-40) REVERT: A 295 LYS cc_start: 0.8396 (tppt) cc_final: 0.8006 (mptp) REVERT: A 409 ARG cc_start: 0.7586 (mmt90) cc_final: 0.7256 (mmm-85) REVERT: A 437 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6665 (tt0) REVERT: A 452 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6435 (mmm) REVERT: A 457 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7496 (tm) REVERT: A 461 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8379 (mp) REVERT: A 472 ARG cc_start: 0.7081 (ttm-80) cc_final: 0.6802 (ttt-90) REVERT: B 73 THR cc_start: 0.8565 (t) cc_final: 0.8212 (p) REVERT: B 196 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6316 (mmtt) REVERT: B 291 SER cc_start: 0.9356 (p) cc_final: 0.9088 (m) REVERT: B 312 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: C 3 LYS cc_start: 0.7968 (mptm) cc_final: 0.7605 (tppt) REVERT: C 14 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: D 215 ARG cc_start: 0.7865 (ttt180) cc_final: 0.7649 (ttm-80) REVERT: D 266 MET cc_start: 0.6667 (mtt) cc_final: 0.6434 (mtt) outliers start: 54 outliers final: 24 residues processed: 156 average time/residue: 1.2120 time to fit residues: 204.5523 Evaluate side-chains 126 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 179 SER Chi-restraints excluded: chain A residue 198 ASN 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 378 LEU 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 196 LYS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 196 ASN ** 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 = 0.3950 r_free = 0.3950 target = 0.173208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141214 restraints weight = 10463.016| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.94 r_work: 0.3406 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3944 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= 0.222 Angle : 0.694 9.902 14130 Z= 0.369 Chirality : 0.047 0.273 1574 Planarity : 0.005 0.090 1790 Dihedral : 6.823 54.591 1372 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.10 % Favored : 91.83 % Rotamer: Outliers : 5.24 % Allowed : 20.24 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.22), residues: 1260 helix: 0.22 (0.26), residues: 379 sheet: -1.26 (0.26), residues: 348 loop : -3.01 (0.23), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 323 HIS 0.006 0.001 HIS A 310 PHE 0.018 0.002 PHE D 331 TYR 0.020 0.002 TYR C 137 ARG 0.004 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 519) hydrogen bonds : angle 4.85749 ( 1863) covalent geometry : bond 0.00516 (10464) covalent geometry : angle 0.69404 (14130) *********************** 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 164 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 104 time to evaluate : 1.078 Fit side-chains REVERT: A 198 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7677 (m-40) REVERT: A 295 LYS cc_start: 0.8343 (tppt) cc_final: 0.8074 (mptp) REVERT: A 316 GLU cc_start: 0.8435 (tt0) cc_final: 0.8163 (tt0) REVERT: A 409 ARG cc_start: 0.7518 (mmt90) cc_final: 0.7205 (mmm-85) REVERT: A 437 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6937 (tt0) REVERT: A 452 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6317 (mmm) REVERT: A 457 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7438 (tm) REVERT: A 461 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8437 (mp) REVERT: A 472 ARG cc_start: 0.7058 (ttm-80) cc_final: 0.6783 (ttt-90) REVERT: B 73 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8218 (p) REVERT: B 115 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8145 (ttm) REVERT: B 155 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7596 (mp) REVERT: B 196 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6391 (mmtt) REVERT: B 291 SER cc_start: 0.9371 (p) cc_final: 0.9083 (m) REVERT: B 312 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: C 3 LYS cc_start: 0.8098 (mptm) cc_final: 0.7646 (tppt) REVERT: C 14 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: C 105 LYS cc_start: 0.7692 (ttmt) cc_final: 0.7436 (tttm) REVERT: C 111 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: C 293 ASP cc_start: 0.7653 (t0) cc_final: 0.7426 (t0) REVERT: D 261 MET cc_start: 0.1578 (mtt) cc_final: 0.0859 (mtp) REVERT: D 266 MET cc_start: 0.6727 (mtt) cc_final: 0.6475 (mtt) REVERT: D 454 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.7715 (ttp-170) outliers start: 60 outliers final: 27 residues processed: 150 average time/residue: 1.2840 time to fit residues: 207.9958 Evaluate side-chains 137 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 1.939 ------------------------------------------------------------------------------- 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 179 SER Chi-restraints excluded: chain A residue 198 ASN 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 378 LEU 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 73 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE 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 D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 257 SER 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 75 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 347 GLN C 296 HIS D 130 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.175780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.143847 restraints weight = 10450.800| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.94 r_work: 0.3440 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10464 Z= 0.146 Angle : 0.619 9.232 14130 Z= 0.332 Chirality : 0.043 0.231 1574 Planarity : 0.005 0.086 1790 Dihedral : 6.408 51.820 1372 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 5.32 % Allowed : 21.55 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.22), residues: 1260 helix: 0.70 (0.27), residues: 379 sheet: -1.17 (0.26), residues: 348 loop : -2.86 (0.23), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 301 HIS 0.005 0.001 HIS B 234 PHE 0.017 0.001 PHE A 237 TYR 0.018 0.001 TYR C 137 ARG 0.004 0.000 ARG A 275 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 519) hydrogen bonds : angle 4.54425 ( 1863) covalent geometry : bond 0.00333 (10464) covalent geometry : angle 0.61900 (14130) *********************** 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 169 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 108 time to evaluate : 1.204 Fit side-chains REVERT: A 295 LYS cc_start: 0.8290 (tppt) cc_final: 0.8003 (mptp) REVERT: A 409 ARG cc_start: 0.7512 (mmt90) cc_final: 0.7228 (mmm-85) REVERT: A 437 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7025 (tt0) REVERT: A 452 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6469 (mmm) REVERT: A 457 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7415 (tm) REVERT: A 461 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8423 (mp) REVERT: A 472 ARG cc_start: 0.6974 (ttm-80) cc_final: 0.6689 (ttt-90) REVERT: B 73 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8253 (p) REVERT: B 291 SER cc_start: 0.9343 (p) cc_final: 0.9063 (m) REVERT: C 3 LYS cc_start: 0.8003 (mptm) cc_final: 0.7464 (tppt) REVERT: C 14 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: C 105 LYS cc_start: 0.7626 (ttmt) cc_final: 0.7371 (tttm) REVERT: D 261 MET cc_start: 0.1459 (mtt) cc_final: 0.0951 (mtp) REVERT: D 266 MET cc_start: 0.6593 (mtt) cc_final: 0.6319 (mtt) outliers start: 61 outliers final: 26 residues processed: 154 average time/residue: 1.0909 time to fit residues: 182.4780 Evaluate side-chains 130 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 257 SER Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER 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 A residue 461 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 155 TYR 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 199 THR Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 248 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 359 SER Chi-restraints excluded: chain D residue 380 ASP 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 90 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN D 130 ASN D 196 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.172031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139837 restraints weight = 10610.011| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.97 r_work: 0.3384 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4201 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= 0.226 Angle : 0.697 9.866 14130 Z= 0.370 Chirality : 0.046 0.270 1574 Planarity : 0.005 0.090 1790 Dihedral : 6.667 47.243 1372 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.33 % Favored : 91.59 % Rotamer: Outliers : 6.11 % Allowed : 21.47 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.22), residues: 1260 helix: 0.62 (0.27), residues: 379 sheet: -1.23 (0.26), residues: 346 loop : -2.77 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 301 HIS 0.006 0.001 HIS A 310 PHE 0.018 0.002 PHE D 331 TYR 0.021 0.002 TYR C 137 ARG 0.006 0.001 ARG A 275 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 519) hydrogen bonds : angle 4.79634 ( 1863) covalent geometry : bond 0.00528 (10464) covalent geometry : angle 0.69714 (14130) *********************** 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 177 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 107 time to evaluate : 1.084 Fit side-chains REVERT: A 198 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7762 (m-40) REVERT: A 295 LYS cc_start: 0.8365 (tppt) cc_final: 0.8066 (mptp) REVERT: A 376 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6321 (mpt-90) REVERT: A 409 ARG cc_start: 0.7583 (mmt90) cc_final: 0.7288 (mmm-85) REVERT: A 437 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: A 452 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6685 (mmm) REVERT: A 461 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8454 (mp) REVERT: A 472 ARG cc_start: 0.7057 (ttm-80) cc_final: 0.6772 (ttt-90) REVERT: B 73 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8001 (p) REVERT: B 115 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8134 (ttm) REVERT: B 173 ASP cc_start: 0.8745 (m-30) cc_final: 0.8370 (m-30) REVERT: B 263 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7494 (mm-30) REVERT: B 291 SER cc_start: 0.9384 (p) cc_final: 0.9070 (m) REVERT: C 3 LYS cc_start: 0.7854 (mptm) cc_final: 0.7395 (tppt) REVERT: C 14 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: C 21 ASP cc_start: 0.7745 (m-30) cc_final: 0.7367 (m-30) REVERT: C 105 LYS cc_start: 0.7744 (ttmt) cc_final: 0.7465 (tttm) REVERT: D 193 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6379 (pm20) REVERT: D 261 MET cc_start: 0.1726 (mtt) cc_final: 0.0967 (mtp) REVERT: D 266 MET cc_start: 0.6727 (mtt) cc_final: 0.6460 (mtt) outliers start: 70 outliers final: 30 residues processed: 163 average time/residue: 1.1777 time to fit residues: 209.4410 Evaluate side-chains 142 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 198 ASN 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 337 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 452 MET 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 73 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE 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 193 GLN Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 276 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN D 196 ASN D 318 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 = 0.3961 r_free = 0.3961 target = 0.174175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.142083 restraints weight = 10479.505| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.96 r_work: 0.3415 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10464 Z= 0.165 Angle : 0.647 9.323 14130 Z= 0.345 Chirality : 0.044 0.243 1574 Planarity : 0.005 0.083 1790 Dihedral : 6.293 43.166 1370 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.62 % Allowed : 22.77 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.23), residues: 1260 helix: 0.85 (0.27), residues: 379 sheet: -1.18 (0.25), residues: 346 loop : -2.72 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 301 HIS 0.005 0.001 HIS D 466 PHE 0.016 0.002 PHE A 237 TYR 0.027 0.002 TYR C 137 ARG 0.007 0.000 ARG A 275 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 519) hydrogen bonds : angle 4.61485 ( 1863) covalent geometry : bond 0.00381 (10464) covalent geometry : angle 0.64662 (14130) *********************** 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 161 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 108 time to evaluate : 1.054 Fit side-chains REVERT: A 295 LYS cc_start: 0.8353 (tppt) cc_final: 0.7556 (ttpt) REVERT: A 377 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7215 (t0) REVERT: A 409 ARG cc_start: 0.7541 (mmt90) cc_final: 0.7228 (mmm-85) REVERT: A 437 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7088 (mt-10) REVERT: A 452 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6694 (mmm) REVERT: A 457 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7801 (tm) REVERT: A 461 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8425 (mp) REVERT: A 472 ARG cc_start: 0.7048 (ttm-80) cc_final: 0.6774 (ttt-90) REVERT: B 73 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8004 (p) REVERT: B 115 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8115 (ttm) REVERT: B 173 ASP cc_start: 0.8713 (m-30) cc_final: 0.8370 (m-30) REVERT: B 263 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7526 (mm-30) REVERT: B 291 SER cc_start: 0.9348 (p) cc_final: 0.9068 (m) REVERT: C 3 LYS cc_start: 0.7783 (mptm) cc_final: 0.7345 (tppt) REVERT: C 14 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: C 21 ASP cc_start: 0.7625 (m-30) cc_final: 0.7176 (m-30) REVERT: C 105 LYS cc_start: 0.7671 (ttmt) cc_final: 0.7400 (tttm) REVERT: D 193 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6353 (pm20) REVERT: D 261 MET cc_start: 0.1441 (mtt) cc_final: 0.0839 (mtp) REVERT: D 266 MET cc_start: 0.6638 (mtt) cc_final: 0.6372 (mtt) REVERT: D 402 LYS cc_start: 0.6034 (tttt) cc_final: 0.5720 (tmtt) outliers start: 53 outliers final: 28 residues processed: 152 average time/residue: 1.0639 time to fit residues: 175.9374 Evaluate side-chains 140 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 257 SER Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 377 ASP 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 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 73 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE 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 142 GLN Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 257 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.172153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140679 restraints weight = 10491.021| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.86 r_work: 0.3386 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10464 Z= 0.242 Angle : 0.721 10.094 14130 Z= 0.382 Chirality : 0.047 0.277 1574 Planarity : 0.006 0.091 1790 Dihedral : 6.589 45.071 1370 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.57 % Favored : 91.35 % Rotamer: Outliers : 4.62 % Allowed : 23.21 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.23), residues: 1260 helix: 0.63 (0.27), residues: 379 sheet: -1.21 (0.26), residues: 344 loop : -2.72 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 301 HIS 0.007 0.002 HIS D 466 PHE 0.021 0.002 PHE D 131 TYR 0.034 0.002 TYR C 137 ARG 0.006 0.001 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 519) hydrogen bonds : angle 4.87724 ( 1863) covalent geometry : bond 0.00569 (10464) covalent geometry : angle 0.72053 (14130) *********************** 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 160 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 107 time to evaluate : 2.312 Fit side-chains REVERT: A 291 MET cc_start: 0.4867 (OUTLIER) cc_final: 0.4609 (mmm) REVERT: A 295 LYS cc_start: 0.8366 (tppt) cc_final: 0.8090 (mptp) REVERT: A 376 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.6305 (mpt-90) REVERT: A 377 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7330 (t0) REVERT: A 409 ARG cc_start: 0.7620 (mmt90) cc_final: 0.7284 (mmm-85) REVERT: A 437 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7209 (mt-10) REVERT: A 452 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6735 (mmm) REVERT: A 461 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8462 (mp) REVERT: A 472 ARG cc_start: 0.7002 (ttm-80) cc_final: 0.6764 (ttt-90) REVERT: B 73 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.7946 (p) REVERT: B 115 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8159 (ttm) REVERT: B 263 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7551 (mm-30) REVERT: B 291 SER cc_start: 0.9371 (p) cc_final: 0.9097 (m) REVERT: C 3 LYS cc_start: 0.7877 (mptm) cc_final: 0.7390 (tppt) REVERT: C 14 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: C 21 ASP cc_start: 0.7720 (m-30) cc_final: 0.7393 (m-30) REVERT: C 105 LYS cc_start: 0.7762 (ttmt) cc_final: 0.7485 (tttm) REVERT: C 297 ARG cc_start: 0.8036 (tpp80) cc_final: 0.7826 (tpt170) REVERT: D 193 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.6300 (pm20) REVERT: D 261 MET cc_start: 0.1788 (mtt) cc_final: 0.0985 (mtp) REVERT: D 266 MET cc_start: 0.6745 (mtt) cc_final: 0.6493 (mtt) REVERT: D 287 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.6728 (mtp180) REVERT: D 402 LYS cc_start: 0.6395 (tttt) cc_final: 0.5971 (tmtt) outliers start: 53 outliers final: 30 residues processed: 150 average time/residue: 1.3020 time to fit residues: 212.7523 Evaluate side-chains 147 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 257 SER 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 337 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 377 ASP 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 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 73 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 102 ILE 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 193 GLN Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 287 ARG 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 35 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 50 optimal weight: 0.0060 chunk 115 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 72 ASN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 433 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.177816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.146268 restraints weight = 10412.206| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.88 r_work: 0.3472 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10464 Z= 0.115 Angle : 0.597 8.372 14130 Z= 0.319 Chirality : 0.042 0.201 1574 Planarity : 0.005 0.077 1790 Dihedral : 5.916 36.729 1370 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.62 % Allowed : 25.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.23), residues: 1260 helix: 1.18 (0.28), residues: 379 sheet: -0.98 (0.25), residues: 364 loop : -2.62 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 301 HIS 0.003 0.001 HIS D 310 PHE 0.019 0.001 PHE A 237 TYR 0.023 0.001 TYR C 112 ARG 0.009 0.001 ARG A 275 Details of bonding type rmsd hydrogen bonds : bond 0.02842 ( 519) hydrogen bonds : angle 4.34663 ( 1863) covalent geometry : bond 0.00259 (10464) covalent geometry : angle 0.59690 (14130) ********************** 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 140 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.318 Fit side-chains REVERT: A 159 ASN cc_start: 0.7260 (m-40) cc_final: 0.7060 (m-40) REVERT: A 291 MET cc_start: 0.4265 (mtp) cc_final: 0.3960 (mmm) REVERT: A 295 LYS cc_start: 0.8107 (tppt) cc_final: 0.7333 (ttpt) REVERT: A 409 ARG cc_start: 0.7581 (mmt90) cc_final: 0.7267 (mmm-85) REVERT: A 452 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6665 (mmm) REVERT: A 461 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8409 (mp) REVERT: A 472 ARG cc_start: 0.6992 (ttm-80) cc_final: 0.6789 (ttm-80) REVERT: B 73 THR cc_start: 0.8395 (t) cc_final: 0.7972 (p) REVERT: B 291 SER cc_start: 0.9268 (p) cc_final: 0.9065 (m) REVERT: C 3 LYS cc_start: 0.7588 (mptm) cc_final: 0.7111 (tppt) REVERT: C 105 LYS cc_start: 0.7637 (ttmt) cc_final: 0.7354 (tttm) REVERT: D 154 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6273 (pp) REVERT: D 261 MET cc_start: 0.1048 (mtt) cc_final: 0.0359 (mtp) REVERT: D 266 MET cc_start: 0.6616 (mtt) cc_final: 0.6362 (mtt) REVERT: D 321 LYS cc_start: 0.7558 (mtpt) cc_final: 0.6713 (tptt) REVERT: D 402 LYS cc_start: 0.6615 (tttt) cc_final: 0.6297 (tmtt) REVERT: D 459 PHE cc_start: 0.8088 (t80) cc_final: 0.7551 (t80) outliers start: 30 outliers final: 15 residues processed: 132 average time/residue: 1.1963 time to fit residues: 171.6105 Evaluate side-chains 118 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 452 MET 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 202 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 173 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 248 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 337 THR 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 11 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 D 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.174307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.141441 restraints weight = 10516.462| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.02 r_work: 0.3412 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10464 Z= 0.164 Angle : 0.645 9.403 14130 Z= 0.343 Chirality : 0.044 0.236 1574 Planarity : 0.005 0.089 1790 Dihedral : 5.879 40.000 1366 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.86 % Favored : 92.06 % Rotamer: Outliers : 2.53 % Allowed : 26.18 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.23), residues: 1260 helix: 1.15 (0.28), residues: 373 sheet: -1.03 (0.25), residues: 368 loop : -2.61 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 301 HIS 0.005 0.001 HIS D 466 PHE 0.016 0.002 PHE A 237 TYR 0.020 0.002 TYR C 137 ARG 0.004 0.001 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 519) hydrogen bonds : angle 4.50486 ( 1863) covalent geometry : bond 0.00380 (10464) covalent geometry : angle 0.64534 (14130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8051.66 seconds wall clock time: 141 minutes 12.06 seconds (8472.06 seconds total)