Starting phenix.real_space_refine on Sun Dec 29 07:07:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7btw_30189/12_2024/7btw_30189.cif Found real_map, /net/cci-nas-00/data/ceres_data/7btw_30189/12_2024/7btw_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_30189/12_2024/7btw_30189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7btw_30189/12_2024/7btw_30189.map" model { file = "/net/cci-nas-00/data/ceres_data/7btw_30189/12_2024/7btw_30189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7btw_30189/12_2024/7btw_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-5532/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: 6.49, 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: 2.70 Conformation dependent library (CDL) restraints added in 1.2 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: 1.25 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: 3.61 Time building geometry restraints manager: 3.11 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.270 Set scattering table: 0.140 Process input model: 26.290 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.750 ------------------------------------------------------------------------------- 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= 0.531 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 *********************** 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 : 1.200 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: 1.1840 time to fit residues: 351.9501 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 : 1.335 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 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= 0.314 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 *********************** 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 : 1.173 Fit side-chains REVERT: A 291 MET cc_start: 0.5340 (ttp) cc_final: 0.4488 (tmt) REVERT: A 295 LYS cc_start: 0.8115 (tppt) cc_final: 0.7643 (ttpt) REVERT: A 409 ARG cc_start: 0.7774 (mmt90) cc_final: 0.7567 (mmm-85) REVERT: A 437 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5126 (mp0) REVERT: A 457 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7295 (tm) REVERT: B 73 THR cc_start: 0.8295 (t) cc_final: 0.8026 (p) REVERT: B 151 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7857 (ttp-110) REVERT: B 196 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.6276 (mmtt) REVERT: B 263 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7133 (mm-30) REVERT: C 3 LYS cc_start: 0.8006 (mptm) cc_final: 0.7795 (tppt) REVERT: C 14 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6136 (mp0) REVERT: C 21 ASP cc_start: 0.7199 (m-30) cc_final: 0.6617 (m-30) REVERT: C 168 ASN cc_start: 0.7901 (t0) cc_final: 0.7629 (t0) REVERT: D 136 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7309 (m-30) outliers start: 45 outliers final: 20 residues processed: 164 average time/residue: 1.1570 time to fit residues: 205.5217 Evaluate side-chains 128 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS A 318 ASN A 476 GLN B 72 ASN B 249 HIS C 84 ASN C 129 GLN D 303 ASN D 369 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3465 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= 0.324 Angle : 0.713 10.358 14130 Z= 0.381 Chirality : 0.047 0.278 1574 Planarity : 0.006 0.093 1790 Dihedral : 7.412 59.619 1377 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.90 % Rotamer: Outliers : 5.15 % Allowed : 18.76 % Favored : 76.09 % 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: -2.86 (0.21), residues: 1260 helix: -0.56 (0.25), residues: 377 sheet: -1.52 (0.25), residues: 357 loop : -3.18 (0.22), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 323 HIS 0.006 0.001 HIS B 234 PHE 0.019 0.002 PHE D 331 TYR 0.021 0.002 TYR C 137 ARG 0.004 0.001 ARG A 208 *********************** 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 176 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 117 time to evaluate : 1.148 Fit side-chains REVERT: A 198 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7419 (m-40) REVERT: A 295 LYS cc_start: 0.8202 (tppt) cc_final: 0.7798 (ttpt) REVERT: A 409 ARG cc_start: 0.7695 (mmt90) cc_final: 0.7418 (mmm-85) REVERT: A 437 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6384 (mt-10) REVERT: A 461 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8399 (mp) REVERT: B 73 THR cc_start: 0.8540 (t) cc_final: 0.8305 (p) REVERT: B 196 LYS cc_start: 0.6664 (OUTLIER) cc_final: 0.6319 (mmtt) REVERT: B 312 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7048 (mt-10) REVERT: C 3 LYS cc_start: 0.8044 (mptm) cc_final: 0.7827 (tppt) REVERT: C 14 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6236 (mp0) REVERT: D 215 ARG cc_start: 0.7297 (ttt180) cc_final: 0.7037 (ttm-80) outliers start: 59 outliers final: 28 residues processed: 165 average time/residue: 1.2885 time to fit residues: 229.2378 Evaluate side-chains 134 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 199 THR 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 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 312 GLU 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 276 THR Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN C 300 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10464 Z= 0.238 Angle : 0.644 9.448 14130 Z= 0.345 Chirality : 0.044 0.240 1574 Planarity : 0.005 0.089 1790 Dihedral : 6.755 53.872 1374 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.80 % Allowed : 20.16 % Favored : 75.04 % 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: -2.34 (0.22), residues: 1260 helix: 0.14 (0.27), residues: 378 sheet: -1.27 (0.25), residues: 358 loop : -3.07 (0.22), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 323 HIS 0.005 0.001 HIS B 234 PHE 0.018 0.002 PHE D 331 TYR 0.018 0.001 TYR C 137 ARG 0.005 0.000 ARG A 472 *********************** 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 177 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 122 time to evaluate : 1.239 Fit side-chains REVERT: A 295 LYS cc_start: 0.8044 (tppt) cc_final: 0.7732 (ttpt) REVERT: A 409 ARG cc_start: 0.7622 (mmt90) cc_final: 0.7414 (mmm-85) REVERT: A 461 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8400 (mp) REVERT: B 196 LYS cc_start: 0.6645 (OUTLIER) cc_final: 0.6244 (mmtt) REVERT: B 291 SER cc_start: 0.9198 (p) cc_final: 0.8894 (m) REVERT: C 3 LYS cc_start: 0.7983 (mptm) cc_final: 0.7759 (tppt) REVERT: C 14 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6190 (mp0) REVERT: D 266 MET cc_start: 0.7358 (mtt) cc_final: 0.6972 (mtt) outliers start: 55 outliers final: 24 residues processed: 163 average time/residue: 1.2033 time to fit residues: 213.0814 Evaluate side-chains 132 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 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 378 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 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 D residue 171 SER Chi-restraints excluded: chain D residue 199 THR 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 380 ASP Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 441 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 314 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3958 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= 0.325 Angle : 0.689 9.849 14130 Z= 0.367 Chirality : 0.046 0.269 1574 Planarity : 0.006 0.093 1790 Dihedral : 6.710 53.927 1370 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.41 % Favored : 91.51 % Rotamer: Outliers : 5.76 % Allowed : 20.59 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.16 % Rama-Z (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: -2.23 (0.22), residues: 1260 helix: 0.32 (0.27), residues: 378 sheet: -1.24 (0.26), residues: 340 loop : -3.00 (0.22), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 323 HIS 0.006 0.001 HIS A 310 PHE 0.019 0.002 PHE D 331 TYR 0.021 0.002 TYR C 137 ARG 0.006 0.001 ARG A 275 *********************** 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 170 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 104 time to evaluate : 1.343 Fit side-chains REVERT: A 295 LYS cc_start: 0.8098 (tppt) cc_final: 0.7779 (ttpt) REVERT: A 376 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6487 (mpt-90) REVERT: A 409 ARG cc_start: 0.7633 (mmt90) cc_final: 0.7415 (mmm-85) REVERT: A 461 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8377 (mp) REVERT: B 196 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.6358 (mmtt) REVERT: B 291 SER cc_start: 0.9206 (p) cc_final: 0.8909 (m) REVERT: C 3 LYS cc_start: 0.8043 (mptm) cc_final: 0.7812 (tppt) REVERT: C 14 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6303 (mp0) REVERT: C 21 ASP cc_start: 0.7236 (m-30) cc_final: 0.6815 (m-30) REVERT: C 111 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6779 (tm-30) REVERT: D 261 MET cc_start: 0.1556 (mtt) cc_final: 0.0915 (mtp) REVERT: D 266 MET cc_start: 0.7332 (mtt) cc_final: 0.6759 (mtt) REVERT: D 287 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.6537 (mtp180) REVERT: D 456 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6630 (mt-10) outliers start: 66 outliers final: 30 residues processed: 153 average time/residue: 1.2280 time to fit residues: 202.9626 Evaluate side-chains 135 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 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 337 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 447 VAL 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 179 ILE Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 202 VAL 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 C residue 284 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10464 Z= 0.294 Angle : 0.668 9.686 14130 Z= 0.357 Chirality : 0.046 0.259 1574 Planarity : 0.006 0.091 1790 Dihedral : 6.616 54.046 1370 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.17 % Favored : 91.75 % Rotamer: Outliers : 5.50 % Allowed : 20.94 % Favored : 73.56 % 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: -2.05 (0.22), residues: 1260 helix: 0.50 (0.27), residues: 379 sheet: -1.21 (0.26), residues: 348 loop : -2.89 (0.23), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 197 HIS 0.005 0.001 HIS D 450 PHE 0.015 0.002 PHE A 237 TYR 0.017 0.002 TYR C 137 ARG 0.005 0.001 ARG A 472 *********************** 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 161 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 98 time to evaluate : 1.190 Fit side-chains REVERT: A 295 LYS cc_start: 0.8088 (tppt) cc_final: 0.7869 (mptp) REVERT: A 321 LYS cc_start: 0.8401 (ttpt) cc_final: 0.8072 (ttpt) REVERT: A 376 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6386 (mpt-90) REVERT: A 409 ARG cc_start: 0.7653 (mmt90) cc_final: 0.7440 (mmm-85) REVERT: A 461 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8352 (mp) REVERT: B 196 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.6344 (mmtt) REVERT: B 263 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: B 291 SER cc_start: 0.9205 (p) cc_final: 0.8913 (m) REVERT: B 312 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7304 (mt-10) REVERT: C 3 LYS cc_start: 0.8017 (mptm) cc_final: 0.7759 (tppt) REVERT: C 14 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6297 (mp0) REVERT: C 21 ASP cc_start: 0.7219 (m-30) cc_final: 0.6732 (m-30) REVERT: C 102 ILE cc_start: 0.8117 (mm) cc_final: 0.7771 (mp) REVERT: C 111 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: D 193 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6200 (pm20) REVERT: D 261 MET cc_start: 0.1785 (mtt) cc_final: 0.1032 (mtp) REVERT: D 266 MET cc_start: 0.7320 (mtt) cc_final: 0.6762 (mtt) REVERT: D 287 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6552 (mtp180) outliers start: 63 outliers final: 33 residues processed: 150 average time/residue: 1.1920 time to fit residues: 193.2683 Evaluate side-chains 132 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 90 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 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 337 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 447 VAL 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 179 ILE 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 263 GLU 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 C residue 284 LEU Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 257 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 68 optimal weight: 0.4980 chunk 102 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 D 130 ASN D 303 ASN D 318 ASN D 450 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10464 Z= 0.212 Angle : 0.618 9.030 14130 Z= 0.330 Chirality : 0.043 0.228 1574 Planarity : 0.005 0.085 1790 Dihedral : 6.323 54.145 1370 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 5.06 % Allowed : 21.99 % Favored : 72.95 % 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: -1.78 (0.23), residues: 1260 helix: 0.84 (0.27), residues: 385 sheet: -1.17 (0.26), residues: 346 loop : -2.77 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 197 HIS 0.004 0.001 HIS B 234 PHE 0.017 0.001 PHE A 237 TYR 0.029 0.001 TYR C 137 ARG 0.006 0.001 ARG A 472 *********************** 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 162 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 104 time to evaluate : 1.499 Fit side-chains REVERT: A 295 LYS cc_start: 0.8047 (tppt) cc_final: 0.7752 (ttpt) REVERT: A 321 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7897 (ttpt) REVERT: A 409 ARG cc_start: 0.7626 (mmt90) cc_final: 0.7388 (mmm-85) REVERT: A 461 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8363 (mp) REVERT: B 291 SER cc_start: 0.9142 (p) cc_final: 0.8898 (m) REVERT: C 3 LYS cc_start: 0.7764 (mptm) cc_final: 0.7531 (tppt) REVERT: C 14 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6257 (mp0) REVERT: C 21 ASP cc_start: 0.7066 (m-30) cc_final: 0.6527 (m-30) REVERT: C 102 ILE cc_start: 0.8051 (mm) cc_final: 0.7722 (mp) REVERT: D 146 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6923 (tt) REVERT: D 193 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6175 (pm20) REVERT: D 261 MET cc_start: 0.1919 (mtt) cc_final: 0.1225 (mtp) REVERT: D 266 MET cc_start: 0.7288 (mtt) cc_final: 0.6724 (mtt) REVERT: D 287 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6322 (mtp180) REVERT: D 459 PHE cc_start: 0.7969 (t80) cc_final: 0.7526 (t80) outliers start: 58 outliers final: 31 residues processed: 149 average time/residue: 1.1457 time to fit residues: 185.0173 Evaluate side-chains 134 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 242 LEU 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 378 LEU Chi-restraints excluded: chain A residue 447 VAL 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 179 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 146 LEU 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 257 SER Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 363 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 72 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 ASN D 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 10464 Z= 0.451 Angle : 0.764 10.444 14130 Z= 0.404 Chirality : 0.049 0.292 1574 Planarity : 0.006 0.093 1790 Dihedral : 6.892 58.184 1370 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.57 % Favored : 91.35 % Rotamer: Outliers : 4.62 % Allowed : 22.25 % Favored : 73.12 % 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: -2.05 (0.22), residues: 1260 helix: 0.53 (0.27), residues: 373 sheet: -1.28 (0.26), residues: 344 loop : -2.81 (0.23), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 197 HIS 0.009 0.002 HIS D 466 PHE 0.018 0.002 PHE D 331 TYR 0.037 0.002 TYR C 137 ARG 0.008 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 102 time to evaluate : 1.309 Fit side-chains REVERT: A 295 LYS cc_start: 0.8122 (tppt) cc_final: 0.7809 (ttpt) REVERT: A 321 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8082 (ttpt) REVERT: A 409 ARG cc_start: 0.7725 (mmt90) cc_final: 0.7459 (mmm-85) REVERT: A 461 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8441 (mt) REVERT: B 291 SER cc_start: 0.9210 (p) cc_final: 0.8930 (m) REVERT: B 312 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: C 3 LYS cc_start: 0.8125 (mptm) cc_final: 0.7882 (tppt) REVERT: C 14 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: C 21 ASP cc_start: 0.7317 (m-30) cc_final: 0.7006 (m-30) REVERT: C 102 ILE cc_start: 0.8200 (mm) cc_final: 0.7908 (mp) REVERT: C 111 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6806 (tm-30) REVERT: D 193 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6281 (pm20) REVERT: D 261 MET cc_start: 0.1921 (mtt) cc_final: 0.1222 (mtp) REVERT: D 266 MET cc_start: 0.7385 (mtt) cc_final: 0.6995 (mtt) REVERT: D 287 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6483 (mtp180) REVERT: D 454 ARG cc_start: 0.8028 (ttt180) cc_final: 0.7798 (ttp-170) outliers start: 53 outliers final: 34 residues processed: 143 average time/residue: 1.1717 time to fit residues: 182.1634 Evaluate side-chains 139 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 447 VAL 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 179 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 239 GLU 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 363 SER Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 470 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 D 130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10464 Z= 0.298 Angle : 0.679 9.404 14130 Z= 0.361 Chirality : 0.046 0.258 1574 Planarity : 0.005 0.086 1790 Dihedral : 6.673 56.532 1370 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.25 % Favored : 91.67 % Rotamer: Outliers : 3.93 % Allowed : 24.08 % Favored : 71.99 % 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: -1.88 (0.23), residues: 1260 helix: 0.69 (0.27), residues: 379 sheet: -1.27 (0.25), residues: 344 loop : -2.70 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 197 HIS 0.007 0.001 HIS D 466 PHE 0.016 0.002 PHE A 237 TYR 0.028 0.002 TYR C 137 ARG 0.006 0.001 ARG A 275 *********************** 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 144 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 99 time to evaluate : 1.204 Fit side-chains REVERT: A 295 LYS cc_start: 0.8014 (tppt) cc_final: 0.7704 (ttpt) REVERT: A 321 LYS cc_start: 0.8298 (ttpt) cc_final: 0.7996 (ttpt) REVERT: A 376 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6534 (mpt-90) REVERT: A 409 ARG cc_start: 0.7707 (mmt90) cc_final: 0.7435 (mmm-85) REVERT: A 461 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8397 (mp) REVERT: B 263 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: B 291 SER cc_start: 0.9175 (p) cc_final: 0.8927 (m) REVERT: C 3 LYS cc_start: 0.8090 (mptm) cc_final: 0.7850 (tppt) REVERT: C 14 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: C 21 ASP cc_start: 0.7213 (m-30) cc_final: 0.6716 (m-30) REVERT: D 193 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6145 (pm20) REVERT: D 261 MET cc_start: 0.1628 (mtt) cc_final: 0.0938 (mtp) REVERT: D 266 MET cc_start: 0.7358 (mtt) cc_final: 0.6913 (mtt) REVERT: D 287 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6368 (mtp180) REVERT: D 452 MET cc_start: 0.7569 (pmt) cc_final: 0.6930 (ptt) REVERT: D 454 ARG cc_start: 0.8029 (ttt180) cc_final: 0.7801 (ttp-170) REVERT: D 466 HIS cc_start: 0.4926 (OUTLIER) cc_final: 0.4377 (t-90) outliers start: 45 outliers final: 30 residues processed: 136 average time/residue: 1.2550 time to fit residues: 184.7154 Evaluate side-chains 135 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 378 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 179 ILE Chi-restraints excluded: chain B residue 202 VAL 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 78 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 247 VAL 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 257 SER 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 363 SER Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 470 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.0170 chunk 56 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN D 130 ASN D 318 ASN D 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4583 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= 0.158 Angle : 0.589 8.138 14130 Z= 0.317 Chirality : 0.042 0.194 1574 Planarity : 0.005 0.081 1790 Dihedral : 5.964 43.530 1370 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.53 % Allowed : 25.65 % 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: -1.39 (0.23), residues: 1260 helix: 1.25 (0.28), residues: 372 sheet: -0.93 (0.25), residues: 370 loop : -2.58 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 197 HIS 0.003 0.001 HIS D 310 PHE 0.020 0.001 PHE A 237 TYR 0.017 0.001 TYR C 137 ARG 0.005 0.000 ARG A 275 ********************** 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 147 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 1.168 Fit side-chains REVERT: A 295 LYS cc_start: 0.7833 (tppt) cc_final: 0.7588 (ttpt) REVERT: A 409 ARG cc_start: 0.7634 (mmt90) cc_final: 0.7422 (mmm-85) REVERT: A 461 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8368 (mp) REVERT: B 162 MET cc_start: 0.7972 (mmt) cc_final: 0.7341 (mmp) REVERT: B 291 SER cc_start: 0.9077 (p) cc_final: 0.8871 (m) REVERT: C 3 LYS cc_start: 0.7602 (mptm) cc_final: 0.7340 (tppt) REVERT: C 21 ASP cc_start: 0.6944 (m-30) cc_final: 0.6334 (m-30) REVERT: C 46 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7644 (pt) REVERT: C 102 ILE cc_start: 0.7997 (mm) cc_final: 0.7665 (mp) REVERT: C 111 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6562 (tm-30) REVERT: D 154 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.6142 (pp) REVERT: D 261 MET cc_start: 0.1615 (mtt) cc_final: 0.0937 (mtp) REVERT: D 266 MET cc_start: 0.7229 (mtt) cc_final: 0.6650 (mtt) REVERT: D 452 MET cc_start: 0.7282 (pmt) cc_final: 0.6703 (ptt) REVERT: D 459 PHE cc_start: 0.7965 (t80) cc_final: 0.7498 (t80) outliers start: 29 outliers final: 12 residues processed: 142 average time/residue: 1.1489 time to fit residues: 177.2539 Evaluate side-chains 129 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 337 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 111 GLU 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 359 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 470 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 9.9990 chunk 92 optimal weight: 0.0040 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 12 optimal weight: 0.0060 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.5810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.177852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.145223 restraints weight = 10407.814| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.96 r_work: 0.3470 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4653 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= 0.174 Angle : 0.606 8.632 14130 Z= 0.324 Chirality : 0.043 0.203 1574 Planarity : 0.005 0.084 1790 Dihedral : 5.539 37.455 1365 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 1.57 % Allowed : 27.92 % Favored : 70.51 % 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: -1.27 (0.23), residues: 1260 helix: 1.39 (0.28), residues: 373 sheet: -0.90 (0.25), residues: 362 loop : -2.52 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 197 HIS 0.004 0.001 HIS B 249 PHE 0.026 0.001 PHE C 80 TYR 0.022 0.001 TYR B 23 ARG 0.007 0.000 ARG A 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3749.25 seconds wall clock time: 68 minutes 24.91 seconds (4104.91 seconds total)