Starting phenix.real_space_refine on Fri Oct 23 10:13:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ta3_10421/10_2026/6ta3_10421.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ta3_10421/10_2026/6ta3_10421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ta3_10421/10_2026/6ta3_10421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ta3_10421/10_2026/6ta3_10421.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ta3_10421/10_2026/6ta3_10421.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ta3_10421/10_2026/6ta3_10421.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ta3_10421/10_2026/6ta3_10421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ta3_10421/10_2026/6ta3_10421.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5952 2.51 5 N 1637 2.21 5 O 1833 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9491 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3372 Classifications: {'peptide': 429} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Chain: "A" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3425 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 415} Chain: "K" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2607 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 322} Chain breaks: 2 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'MZK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.94, per 1000 atoms: 0.20 Number of scatterers: 9491 At special positions: 0 Unit cell: (70.85, 103.55, 111.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 P 6 15.00 Mg 2 11.99 F 3 9.00 O 1833 8.00 N 1637 7.00 C 5952 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 264.9 milliseconds 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2226 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 11 sheets defined 52.7% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.584A pdb=" N GLY B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 51 Processing helix chain 'B' and resid 69 through 79 removed outlier: 3.932A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 127 removed outlier: 4.282A pdb=" N ALA B 110 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.567A pdb=" N LEU B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR B 159 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 196 removed outlier: 4.045A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 216 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.618A pdb=" N VAL B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.514A pdb=" N LEU B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.539A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 392 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.782A pdb=" N GLU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.597A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.813A pdb=" N GLN A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 129 removed outlier: 4.339A pdb=" N GLU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 Processing helix chain 'A' and resid 181 through 198 removed outlier: 4.027A pdb=" N TYR A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 223 through 244 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.677A pdb=" N GLU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 381 through 402 removed outlier: 3.890A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 412 removed outlier: 3.795A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 Processing helix chain 'K' and resid 29 through 36 Processing helix chain 'K' and resid 77 through 96 removed outlier: 3.695A pdb=" N CYS K 87 " --> pdb=" O ARG K 83 " (cutoff:3.500A) Proline residue: K 88 - end of helix removed outlier: 3.503A pdb=" N GLU K 92 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 117 removed outlier: 3.549A pdb=" N GLY K 117 " --> pdb=" O PHE K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 151 removed outlier: 3.601A pdb=" N LEU K 140 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS K 141 " --> pdb=" O PRO K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 222 removed outlier: 4.247A pdb=" N VAL K 210 " --> pdb=" O ASN K 206 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA K 219 " --> pdb=" O GLU K 215 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS K 220 " --> pdb=" O LYS K 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 276 Processing helix chain 'K' and resid 278 through 305 Processing helix chain 'K' and resid 310 through 313 Processing helix chain 'K' and resid 314 through 320 Processing helix chain 'K' and resid 321 through 324 Processing helix chain 'K' and resid 342 through 359 removed outlier: 3.549A pdb=" N THR K 346 " --> pdb=" O ASN K 342 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS K 357 " --> pdb=" O ALA K 353 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN K 358 " --> pdb=" O HIS K 354 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE K 359 " --> pdb=" O ARG K 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 65 removed outlier: 5.873A pdb=" N VAL B 5 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N THR B 136 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE B 7 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N SER B 138 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 267 through 270 removed outlier: 3.527A pdb=" N GLY B 369 " --> pdb=" O MET B 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 314 through 317 Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 67 removed outlier: 5.661A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 273 Processing sheet with id=AA8, first strand: chain 'K' and resid 70 through 72 removed outlier: 3.669A pdb=" N MET K 70 " --> pdb=" O VAL K 21 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN K 98 " --> pdb=" O ARG K 329 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER K 331 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR K 100 " --> pdb=" O SER K 331 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE K 333 " --> pdb=" O THR K 100 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE K 102 " --> pdb=" O ILE K 333 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR K 335 " --> pdb=" O PHE K 102 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR K 104 " --> pdb=" O THR K 335 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 70 through 72 removed outlier: 3.669A pdb=" N MET K 70 " --> pdb=" O VAL K 21 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN K 98 " --> pdb=" O ARG K 329 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER K 331 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR K 100 " --> pdb=" O SER K 331 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE K 333 " --> pdb=" O THR K 100 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE K 102 " --> pdb=" O ILE K 333 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR K 335 " --> pdb=" O PHE K 102 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR K 104 " --> pdb=" O THR K 335 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL K 158 " --> pdb=" O ILE K 202 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE K 202 " --> pdb=" O VAL K 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 42 through 44 Processing sheet with id=AB2, first strand: chain 'K' and resid 183 through 187 removed outlier: 4.264A pdb=" N GLN K 183 " --> pdb=" O LYS K 197 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLY K 193 " --> pdb=" O ASP K 187 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.91: 1 0.91 - 1.14: 3 1.14 - 1.36: 3087 1.36 - 1.59: 6495 1.59 - 1.82: 95 Bond restraints: 9681 Sorted by residual: bond pdb=" CB SER K 84 " pdb=" OG SER K 84 " ideal model delta sigma weight residual 1.417 0.678 0.739 2.00e-02 2.50e+03 1.37e+03 bond pdb=" CB GLU K 254 " pdb=" CG GLU K 254 " ideal model delta sigma weight residual 1.520 1.061 0.459 3.00e-02 1.11e+03 2.35e+02 bond pdb=" C3A G2P A 501 " pdb=" PB G2P A 501 " ideal model delta sigma weight residual 1.850 1.591 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C THR K 306 " pdb=" O THR K 306 " ideal model delta sigma weight residual 1.234 1.083 0.151 1.26e-02 6.30e+03 1.43e+02 bond pdb=" C3A G2P A 501 " pdb=" PA G2P A 501 " ideal model delta sigma weight residual 1.818 1.592 0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 9676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.76: 12991 6.76 - 13.52: 125 13.52 - 20.28: 6 20.28 - 27.04: 3 27.04 - 33.80: 3 Bond angle restraints: 13128 Sorted by residual: angle pdb=" CA GLY B 10 " pdb=" C GLY B 10 " pdb=" N GLN B 11 " ideal model delta sigma weight residual 115.13 148.93 -33.80 1.05e+00 9.07e-01 1.04e+03 angle pdb=" O GLY B 10 " pdb=" C GLY B 10 " pdb=" N GLN B 11 " ideal model delta sigma weight residual 122.56 90.86 31.70 1.15e+00 7.56e-01 7.60e+02 angle pdb=" CA SER K 84 " pdb=" CB SER K 84 " pdb=" OG SER K 84 " ideal model delta sigma weight residual 111.10 139.29 -28.19 2.00e+00 2.50e-01 1.99e+02 angle pdb=" CA GLU K 254 " pdb=" CB GLU K 254 " pdb=" CG GLU K 254 " ideal model delta sigma weight residual 114.10 139.62 -25.52 2.00e+00 2.50e-01 1.63e+02 angle pdb=" N ASN K 289 " pdb=" CA ASN K 289 " pdb=" C ASN K 289 " ideal model delta sigma weight residual 111.07 99.23 11.84 1.07e+00 8.73e-01 1.22e+02 ... (remaining 13123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.36: 5025 18.36 - 36.72: 493 36.72 - 55.08: 178 55.08 - 73.44: 80 73.44 - 91.80: 14 Dihedral angle restraints: 5790 sinusoidal: 2325 harmonic: 3465 Sorted by residual: dihedral pdb=" CA GLY K 110 " pdb=" C GLY K 110 " pdb=" N LYS K 111 " pdb=" CA LYS K 111 " ideal model delta harmonic sigma weight residual 180.00 137.42 42.58 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" CA GLN B 15 " pdb=" C GLN B 15 " pdb=" N ILE B 16 " pdb=" CA ILE B 16 " ideal model delta harmonic sigma weight residual -180.00 -146.07 -33.93 0 5.00e+00 4.00e-02 4.61e+01 dihedral pdb=" N THR B 143 " pdb=" C THR B 143 " pdb=" CA THR B 143 " pdb=" CB THR B 143 " ideal model delta harmonic sigma weight residual 123.40 138.49 -15.09 0 2.50e+00 1.60e-01 3.64e+01 ... (remaining 5787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 1413 0.183 - 0.365: 43 0.365 - 0.548: 3 0.548 - 0.731: 1 0.731 - 0.913: 1 Chirality restraints: 1461 Sorted by residual: chirality pdb=" CG LEU K 266 " pdb=" CB LEU K 266 " pdb=" CD1 LEU K 266 " pdb=" CD2 LEU K 266 " both_signs ideal model delta sigma weight residual False -2.59 -1.68 -0.91 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" CA THR B 143 " pdb=" N THR B 143 " pdb=" C THR B 143 " pdb=" CB THR B 143 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA PRO K 137 " pdb=" N PRO K 137 " pdb=" C PRO K 137 " pdb=" CB PRO K 137 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.48 2.00e-01 2.50e+01 5.87e+00 ... (remaining 1458 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 399 " -0.268 2.00e-02 2.50e+03 1.90e-01 7.21e+02 pdb=" CG TYR A 399 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 399 " 0.091 2.00e-02 2.50e+03 pdb=" CD2 TYR A 399 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 TYR A 399 " 0.170 2.00e-02 2.50e+03 pdb=" CE2 TYR A 399 " 0.155 2.00e-02 2.50e+03 pdb=" CZ TYR A 399 " 0.109 2.00e-02 2.50e+03 pdb=" OH TYR A 399 " -0.369 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 345 " -0.043 2.00e-02 2.50e+03 9.65e-02 9.30e+01 pdb=" CD GLU K 345 " 0.167 2.00e-02 2.50e+03 pdb=" OE1 GLU K 345 " -0.063 2.00e-02 2.50e+03 pdb=" OE2 GLU K 345 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 104 " -0.128 2.00e-02 2.50e+03 6.80e-02 9.24e+01 pdb=" CG TYR K 104 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR K 104 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR K 104 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 TYR K 104 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR K 104 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR K 104 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR K 104 " -0.085 2.00e-02 2.50e+03 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 0.44 - 1.33: 14 1.33 - 2.22: 108 2.22 - 3.12: 13174 3.12 - 4.01: 31101 4.01 - 4.90: 53116 Warning: very small nonbonded interaction distances. Nonbonded interactions: 97513 Sorted by model distance: nonbonded pdb=" OD1 ASN B 99 " pdb=" PG G2P B 501 " model vdw 0.439 2.720 nonbonded pdb=" O PRO B 259 " pdb=" CD1 PHE A 404 " model vdw 0.578 3.340 nonbonded pdb=" CD LYS B 350 " pdb=" O THR A 179 " model vdw 0.861 3.440 nonbonded pdb=" CG PHE B 260 " pdb=" CE1 HIS A 406 " model vdw 0.923 3.480 nonbonded pdb=" CE LYS B 324 " pdb=" CA ARG A 221 " model vdw 0.951 3.096 ... (remaining 97508 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.460 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.640 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4896 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 : 0.033 1.113 9692 Z= 2.756 Angle : 2.453 33.803 13128 Z= 1.751 Chirality : 0.078 0.913 1461 Planarity : 0.013 0.190 1703 Dihedral : 18.763 91.805 3564 Min Nonbonded Distance : 0.439 Molprobity Statistics. All-atom Clashscore : 210.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 16.02 % Allowed : 16.99 % Favored : 66.99 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.22), residues: 1191 helix: 2.57 (0.20), residues: 558 sheet: 1.18 (0.37), residues: 171 loop : -0.45 (0.23), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.086 0.002 ARG A 402 TYR 0.369 0.011 TYR A 399 PHE 0.033 0.002 PHE K 113 TRP 0.020 0.004 TRP B 344 HIS 0.004 0.000 HIS K 354 Details of bonding type rmsd/Z covalent geometry : bond 0.02375 / 1.60 ( 9681) covalent geometry : angle 2.45329 / 1.75 (13128) hydrogen bonds : bond 0.23958 / 16.65 ( 499) hydrogen bonds : angle 9.07906 / 6.96 ( 1551) Misc. bond : bond 0.66562 / 35.17 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 208 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7762 (mttt) REVERT: B 210 ILE cc_start: 0.8044 (mt) cc_final: 0.7731 (mm) REVERT: B 336 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7156 (mttt) REVERT: B 359 ARG cc_start: 0.6333 (mtt180) cc_final: 0.4899 (mtt180) REVERT: A 22 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6641 (tm-30) REVERT: A 164 LYS cc_start: 0.4698 (OUTLIER) cc_final: 0.3090 (mmtp) REVERT: A 212 ILE cc_start: 0.8030 (mm) cc_final: 0.7752 (mm) REVERT: A 220 GLU cc_start: 0.3323 (OUTLIER) cc_final: 0.2572 (pp20) REVERT: A 266 HIS cc_start: 0.6925 (m90) cc_final: 0.6325 (m90) REVERT: A 303 VAL cc_start: 0.8192 (p) cc_final: 0.7285 (p) REVERT: A 396 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7718 (t0) outliers start: 165 outliers final: 67 residues processed: 337 average time/residue: 0.1256 time to fit residues: 55.0551 Evaluate side-chains 181 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 108 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 33 ARG Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 189 ARG Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117] chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 GLN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 280 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN A 31 GLN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS A 176 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN A 283 HIS A 301 GLN ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.089474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.074987 restraints weight = 44415.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.077468 restraints weight = 24950.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.079112 restraints weight = 15980.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.080246 restraints weight = 11432.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.080852 restraints weight = 8839.862| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.292 9692 Z= 0.353 Angle : 1.086 16.452 13128 Z= 0.579 Chirality : 0.060 0.403 1461 Planarity : 0.010 0.104 1703 Dihedral : 14.714 86.814 1530 Min Nonbonded Distance : 1.594 Molprobity Statistics. All-atom Clashscore : 47.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.35 % Favored : 97.57 % Rotamer: Outliers : 11.94 % Allowed : 20.39 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.22), residues: 1191 helix: 0.01 (0.19), residues: 574 sheet: 1.11 (0.37), residues: 185 loop : -0.58 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 251 TYR 0.144 0.005 TYR A 224 PHE 0.050 0.004 PHE B 260 TRP 0.010 0.003 TRP A 407 HIS 0.014 0.003 HIS A 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00764 / 0.35 ( 9681) covalent geometry : angle 1.08614 / 0.58 (13128) hydrogen bonds : bond 0.08106 / 5.65 ( 499) hydrogen bonds : angle 7.06548 / 5.35 ( 1551) Misc. bond : bond 0.01630 / 1.18 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 165 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6965 (pp20) REVERT: B 23 VAL cc_start: 0.8704 (p) cc_final: 0.8088 (m) REVERT: B 31 ASP cc_start: 0.3209 (OUTLIER) cc_final: 0.2898 (t0) REVERT: B 122 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.7852 (mtpt) REVERT: B 147 MET cc_start: 0.7172 (pmm) cc_final: 0.6781 (pmm) REVERT: B 155 ILE cc_start: 0.7652 (pt) cc_final: 0.7331 (tp) REVERT: B 158 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6115 (mp0) REVERT: B 227 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.7265 (t-170) REVERT: B 228 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8233 (tt) REVERT: B 280 GLN cc_start: 0.7284 (pt0) cc_final: 0.7032 (pt0) REVERT: B 291 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8452 (pp30) REVERT: B 336 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8170 (mttt) REVERT: B 363 MET cc_start: 0.8167 (mpp) cc_final: 0.7940 (mpp) REVERT: A 52 PHE cc_start: 0.6172 (m-10) cc_final: 0.5777 (m-10) REVERT: A 204 VAL cc_start: 0.5752 (OUTLIER) cc_final: 0.5435 (p) REVERT: A 212 ILE cc_start: 0.8105 (mm) cc_final: 0.7775 (mm) REVERT: A 220 GLU cc_start: 0.4812 (OUTLIER) cc_final: 0.3461 (pp20) REVERT: A 242 LEU cc_start: 0.5838 (OUTLIER) cc_final: 0.5484 (tm) REVERT: A 318 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8348 (mm) REVERT: A 338 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8085 (tppp) REVERT: A 371 VAL cc_start: 0.4158 (OUTLIER) cc_final: 0.3912 (t) REVERT: A 404 PHE cc_start: 0.7074 (m-10) cc_final: 0.6606 (m-80) REVERT: K 101 ILE cc_start: 0.9248 (mt) cc_final: 0.9021 (tp) REVERT: K 177 ASP cc_start: 0.7735 (t70) cc_final: 0.7386 (t70) REVERT: K 184 MET cc_start: 0.7106 (tmm) cc_final: 0.6698 (tmm) REVERT: K 261 LEU cc_start: 0.9359 (tp) cc_final: 0.9101 (tp) REVERT: K 263 LEU cc_start: 0.8876 (mm) cc_final: 0.8333 (mt) REVERT: K 290 GLN cc_start: 0.8819 (pp30) cc_final: 0.8207 (pt0) REVERT: K 304 GLU cc_start: 0.8588 (tp30) cc_final: 0.8379 (tp30) outliers start: 123 outliers final: 51 residues processed: 256 average time/residue: 0.1154 time to fit residues: 39.5626 Evaluate side-chains 188 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 123 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain K residue 33 ARG Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain K residue 342 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [74, 99, 86, 60, 66, 69, 95, 102, 105, 41, 82] chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 0.0050 chunk 95 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN A 233 GLN A 393 HIS ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 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 = 0.4272 r_free = 0.4272 target = 0.088495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.073725 restraints weight = 44742.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.076051 restraints weight = 25430.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.077532 restraints weight = 16622.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.078590 restraints weight = 12173.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.079239 restraints weight = 9610.399| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.7137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 9692 Z= 0.233 Angle : 0.898 16.304 13128 Z= 0.466 Chirality : 0.051 0.373 1461 Planarity : 0.008 0.087 1703 Dihedral : 12.074 90.678 1430 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 37.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.43 % Favored : 97.48 % Rotamer: Outliers : 9.71 % Allowed : 22.62 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.22), residues: 1191 helix: 0.03 (0.19), residues: 569 sheet: 0.65 (0.36), residues: 194 loop : -0.80 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 156 TYR 0.145 0.003 TYR A 224 PHE 0.025 0.003 PHE A 267 TRP 0.032 0.003 TRP B 101 HIS 0.011 0.002 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 ( 9681) covalent geometry : angle 0.89810 / 0.47 (13128) hydrogen bonds : bond 0.06651 / 4.70 ( 499) hydrogen bonds : angle 6.43887 / 4.91 ( 1551) Misc. bond : bond 0.01536 / 1.13 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 147 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.6282 (OUTLIER) cc_final: 0.5995 (mm-30) REVERT: B 22 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6661 (pt0) REVERT: B 114 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8168 (t0) REVERT: B 122 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8013 (mtmt) REVERT: B 155 ILE cc_start: 0.7773 (pt) cc_final: 0.7443 (mm) REVERT: B 233 MET cc_start: 0.6879 (mtp) cc_final: 0.5887 (tpp) REVERT: B 280 GLN cc_start: 0.7115 (pt0) cc_final: 0.6493 (pp30) REVERT: B 293 MET cc_start: 0.7491 (mmt) cc_final: 0.6275 (ppp) REVERT: B 331 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8199 (pp) REVERT: B 336 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8193 (mttt) REVERT: B 376 GLU cc_start: 0.4891 (OUTLIER) cc_final: 0.4321 (mp0) REVERT: B 379 LYS cc_start: 0.8490 (pttp) cc_final: 0.8241 (pttp) REVERT: A 52 PHE cc_start: 0.6038 (m-10) cc_final: 0.5263 (m-10) REVERT: A 182 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7843 (p) REVERT: A 205 ASP cc_start: 0.6534 (OUTLIER) cc_final: 0.6194 (m-30) REVERT: A 209 ILE cc_start: 0.7488 (mt) cc_final: 0.6836 (mt) REVERT: A 212 ILE cc_start: 0.8144 (mm) cc_final: 0.7824 (mm) REVERT: A 242 LEU cc_start: 0.5545 (OUTLIER) cc_final: 0.5212 (tm) REVERT: A 267 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.5816 (p90) REVERT: A 311 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6710 (mppt) REVERT: A 404 PHE cc_start: 0.6768 (m-10) cc_final: 0.6122 (m-80) REVERT: A 432 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.6005 (t80) REVERT: K 177 ASP cc_start: 0.7864 (t70) cc_final: 0.7528 (t70) REVERT: K 290 GLN cc_start: 0.8771 (pp30) cc_final: 0.8341 (pt0) REVERT: K 367 GLN cc_start: 0.6629 (OUTLIER) cc_final: 0.5846 (tm-30) outliers start: 100 outliers final: 41 residues processed: 220 average time/residue: 0.1101 time to fit residues: 32.8316 Evaluate side-chains 176 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 121 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 33 ARG Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 367 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [77, 9, 73, 80, 113, 41, 90, 31, 66, 97, 109] chunk 77 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 41 optimal weight: 0.0870 chunk 90 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 109 optimal weight: 0.0070 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.087646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.072798 restraints weight = 44694.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.075028 restraints weight = 25559.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.076552 restraints weight = 16852.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.077544 restraints weight = 12257.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.078250 restraints weight = 9759.215| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.7920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9692 Z= 0.214 Angle : 0.878 21.101 13128 Z= 0.452 Chirality : 0.047 0.249 1461 Planarity : 0.008 0.127 1703 Dihedral : 11.025 85.521 1394 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 32.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 8.25 % Allowed : 23.59 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.22), residues: 1191 helix: 0.04 (0.19), residues: 587 sheet: 0.41 (0.36), residues: 197 loop : -0.98 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 241 TYR 0.140 0.003 TYR A 224 PHE 0.024 0.003 PHE B 385 TRP 0.013 0.002 TRP A 388 HIS 0.013 0.002 HIS K 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 ( 9681) covalent geometry : angle 0.87840 / 0.45 (13128) hydrogen bonds : bond 0.06072 / 4.28 ( 499) hydrogen bonds : angle 6.14004 / 4.64 ( 1551) Misc. bond : bond 0.01479 / 1.11 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 128 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.6140 (mm-30) REVERT: B 103 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7655 (mttt) REVERT: B 114 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8079 (t0) REVERT: B 122 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8087 (mtmt) REVERT: B 233 MET cc_start: 0.6871 (mtp) cc_final: 0.6053 (tpp) REVERT: B 252 LYS cc_start: 0.5065 (OUTLIER) cc_final: 0.4251 (ptmt) REVERT: B 270 PHE cc_start: 0.6556 (t80) cc_final: 0.6077 (t80) REVERT: B 280 GLN cc_start: 0.7093 (pt0) cc_final: 0.6573 (pp30) REVERT: B 293 MET cc_start: 0.7520 (mmt) cc_final: 0.6373 (ppp) REVERT: B 336 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8248 (mttt) REVERT: A 52 PHE cc_start: 0.6176 (m-10) cc_final: 0.5478 (m-10) REVERT: A 188 ILE cc_start: 0.7365 (mp) cc_final: 0.7138 (mt) REVERT: A 209 ILE cc_start: 0.7614 (mt) cc_final: 0.7335 (mt) REVERT: A 212 ILE cc_start: 0.8289 (mm) cc_final: 0.7999 (pt) REVERT: A 220 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.5309 (pp20) REVERT: A 242 LEU cc_start: 0.5451 (OUTLIER) cc_final: 0.5122 (tm) REVERT: A 267 PHE cc_start: 0.6862 (OUTLIER) cc_final: 0.5816 (p90) REVERT: A 311 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6812 (mppt) REVERT: A 313 MET cc_start: 0.5806 (mtp) cc_final: 0.4980 (mtt) REVERT: A 425 MET cc_start: 0.9054 (mmm) cc_final: 0.8746 (mmm) REVERT: A 432 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6010 (t80) REVERT: K 177 ASP cc_start: 0.7894 (t70) cc_final: 0.7550 (t70) REVERT: K 239 PHE cc_start: 0.8314 (t80) cc_final: 0.7937 (t80) REVERT: K 261 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9137 (tp) REVERT: K 290 GLN cc_start: 0.8730 (pp30) cc_final: 0.8493 (tm-30) REVERT: K 367 GLN cc_start: 0.6631 (OUTLIER) cc_final: 0.5561 (tm-30) outliers start: 85 outliers final: 42 residues processed: 190 average time/residue: 0.1042 time to fit residues: 27.3787 Evaluate side-chains 177 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 122 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 367 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [46, 116, 1, 92, 50, 107, 109, 3, 100, 11, 76] chunk 46 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 3 optimal weight: 0.0050 chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 overall best weight: 0.5172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN A 11 GLN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.086498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.071694 restraints weight = 45010.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.073895 restraints weight = 25598.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.075353 restraints weight = 16752.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.076226 restraints weight = 12192.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.076963 restraints weight = 9839.622| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.8575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 9692 Z= 0.206 Angle : 0.839 16.220 13128 Z= 0.428 Chirality : 0.047 0.254 1461 Planarity : 0.007 0.084 1703 Dihedral : 10.181 81.899 1382 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 29.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 7.09 % Allowed : 24.66 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.23), residues: 1191 helix: 0.05 (0.20), residues: 590 sheet: 0.34 (0.36), residues: 196 loop : -1.01 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG B 251 TYR 0.139 0.003 TYR A 224 PHE 0.028 0.003 PHE B 260 TRP 0.026 0.002 TRP B 21 HIS 0.017 0.002 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 ( 9681) covalent geometry : angle 0.83933 / 0.43 (13128) hydrogen bonds : bond 0.05758 / 4.06 ( 499) hydrogen bonds : angle 5.95856 / 4.48 ( 1551) Misc. bond : bond 0.01509 / 1.12 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 129 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.6207 (mm-30) REVERT: B 103 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7615 (mttt) REVERT: B 122 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8071 (mtmt) REVERT: B 257 MET cc_start: 0.8743 (tpp) cc_final: 0.8337 (mmp) REVERT: B 270 PHE cc_start: 0.6358 (t80) cc_final: 0.6079 (t80) REVERT: B 293 MET cc_start: 0.7703 (mmt) cc_final: 0.6590 (ppp) REVERT: B 334 GLN cc_start: 0.7212 (pm20) cc_final: 0.6701 (pp30) REVERT: B 336 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8267 (mttt) REVERT: B 378 PHE cc_start: 0.8313 (m-10) cc_final: 0.8103 (m-10) REVERT: B 379 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8218 (pttp) REVERT: A 52 PHE cc_start: 0.6091 (m-10) cc_final: 0.5531 (m-10) REVERT: A 209 ILE cc_start: 0.7580 (mt) cc_final: 0.7126 (mt) REVERT: A 212 ILE cc_start: 0.8269 (mm) cc_final: 0.7969 (mm) REVERT: A 220 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.5643 (pp20) REVERT: A 242 LEU cc_start: 0.5485 (OUTLIER) cc_final: 0.5211 (tm) REVERT: A 267 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.5795 (p90) REVERT: A 308 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6553 (mpt180) REVERT: A 313 MET cc_start: 0.5875 (mtp) cc_final: 0.5044 (mtt) REVERT: A 425 MET cc_start: 0.8956 (mmm) cc_final: 0.8669 (mmm) REVERT: A 432 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.5911 (t80) REVERT: K 177 ASP cc_start: 0.7994 (t70) cc_final: 0.7647 (t70) REVERT: K 215 GLU cc_start: 0.5502 (OUTLIER) cc_final: 0.4963 (pm20) REVERT: K 245 MET cc_start: 0.8409 (mtm) cc_final: 0.7948 (mpp) REVERT: K 290 GLN cc_start: 0.8842 (pp30) cc_final: 0.8570 (pt0) REVERT: K 367 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.5626 (tm-30) outliers start: 73 outliers final: 45 residues processed: 177 average time/residue: 0.1074 time to fit residues: 25.9822 Evaluate side-chains 174 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 117 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 367 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [10, 89, 61, 56, 107, 85, 102, 7, 113, 59, 70] chunk 10 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 226 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** 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 = 0.4181 r_free = 0.4181 target = 0.083872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.069162 restraints weight = 44823.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.071247 restraints weight = 25779.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.072664 restraints weight = 17087.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.073577 restraints weight = 12546.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.074192 restraints weight = 10085.866| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.9121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9692 Z= 0.220 Angle : 0.823 16.151 13128 Z= 0.423 Chirality : 0.047 0.335 1461 Planarity : 0.008 0.119 1703 Dihedral : 9.922 78.644 1374 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 28.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.98 % Rotamer: Outliers : 7.67 % Allowed : 24.66 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.23), residues: 1191 helix: 0.20 (0.20), residues: 585 sheet: 0.22 (0.36), residues: 198 loop : -0.93 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 33 TYR 0.139 0.003 TYR A 224 PHE 0.042 0.003 PHE B 167 TRP 0.021 0.002 TRP A 407 HIS 0.015 0.002 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 ( 9681) covalent geometry : angle 0.82323 / 0.42 (13128) hydrogen bonds : bond 0.05921 / 4.17 ( 499) hydrogen bonds : angle 5.85418 / 4.43 ( 1551) Misc. bond : bond 0.01533 / 1.12 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 127 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6191 (mm-30) REVERT: B 103 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7725 (mttt) REVERT: B 122 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8140 (mtmt) REVERT: B 216 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7012 (mtmm) REVERT: B 257 MET cc_start: 0.8928 (tpp) cc_final: 0.8529 (mmp) REVERT: B 270 PHE cc_start: 0.6615 (t80) cc_final: 0.6241 (t80) REVERT: B 293 MET cc_start: 0.7816 (mmt) cc_final: 0.6683 (ppp) REVERT: B 299 MET cc_start: 0.7587 (mmm) cc_final: 0.7356 (tpp) REVERT: B 379 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8096 (pttp) REVERT: A 52 PHE cc_start: 0.5919 (m-10) cc_final: 0.5485 (m-10) REVERT: A 132 LEU cc_start: 0.7196 (mp) cc_final: 0.6408 (mt) REVERT: A 209 ILE cc_start: 0.7458 (mt) cc_final: 0.6917 (mt) REVERT: A 212 ILE cc_start: 0.8235 (mm) cc_final: 0.7907 (mm) REVERT: A 220 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.5556 (pp20) REVERT: A 242 LEU cc_start: 0.5505 (OUTLIER) cc_final: 0.5223 (tm) REVERT: A 267 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.5880 (p90) REVERT: A 308 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6684 (mpt180) REVERT: A 313 MET cc_start: 0.6016 (mtp) cc_final: 0.5237 (mtt) REVERT: A 425 MET cc_start: 0.9179 (mmm) cc_final: 0.8870 (mmm) REVERT: A 432 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6023 (t80) REVERT: K 70 MET cc_start: 0.8014 (tpp) cc_final: 0.7752 (tpp) REVERT: K 115 MET cc_start: 0.7582 (tpt) cc_final: 0.7366 (ptt) REVERT: K 177 ASP cc_start: 0.7992 (t70) cc_final: 0.7660 (t70) REVERT: K 215 GLU cc_start: 0.5321 (OUTLIER) cc_final: 0.4825 (pm20) REVERT: K 245 MET cc_start: 0.8419 (mtm) cc_final: 0.7940 (mpp) REVERT: K 344 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8540 (mm-30) REVERT: K 367 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.5717 (tm-30) outliers start: 79 outliers final: 52 residues processed: 190 average time/residue: 0.1105 time to fit residues: 28.3263 Evaluate side-chains 177 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 112 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 344 GLU Chi-restraints excluded: chain K residue 367 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [54, 31, 63, 19, 82, 20, 74, 29, 15, 13, 27] chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 ASN K 367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.083712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.069067 restraints weight = 44831.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.071158 restraints weight = 25383.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.072548 restraints weight = 16737.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.073488 restraints weight = 12313.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.074131 restraints weight = 9849.520| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.9616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9692 Z= 0.198 Angle : 0.829 16.147 13128 Z= 0.417 Chirality : 0.046 0.330 1461 Planarity : 0.007 0.094 1703 Dihedral : 9.705 81.347 1370 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 7.18 % Allowed : 25.15 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.23), residues: 1191 helix: 0.24 (0.20), residues: 586 sheet: 0.21 (0.36), residues: 193 loop : -0.93 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 251 TYR 0.136 0.003 TYR A 224 PHE 0.034 0.003 PHE B 378 TRP 0.015 0.002 TRP B 21 HIS 0.014 0.002 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 9681) covalent geometry : angle 0.82944 / 0.42 (13128) hydrogen bonds : bond 0.05605 / 3.95 ( 499) hydrogen bonds : angle 5.78788 / 4.36 ( 1551) Misc. bond : bond 0.01466 / 1.09 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 125 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6265 (mm-30) REVERT: B 103 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7628 (mttt) REVERT: B 122 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8252 (mtmt) REVERT: B 216 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6945 (mtmm) REVERT: B 257 MET cc_start: 0.8861 (tpp) cc_final: 0.8493 (mmp) REVERT: B 270 PHE cc_start: 0.6729 (t80) cc_final: 0.6441 (t80) REVERT: B 293 MET cc_start: 0.7880 (mmt) cc_final: 0.6866 (ppp) REVERT: A 52 PHE cc_start: 0.5628 (m-10) cc_final: 0.5425 (m-10) REVERT: A 132 LEU cc_start: 0.7496 (mp) cc_final: 0.6742 (mt) REVERT: A 212 ILE cc_start: 0.8273 (mm) cc_final: 0.7962 (mm) REVERT: A 220 GLU cc_start: 0.5965 (OUTLIER) cc_final: 0.5500 (pp20) REVERT: A 242 LEU cc_start: 0.5418 (OUTLIER) cc_final: 0.5182 (tm) REVERT: A 267 PHE cc_start: 0.6799 (OUTLIER) cc_final: 0.5792 (p90) REVERT: A 308 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6779 (mpt180) REVERT: A 313 MET cc_start: 0.6178 (mtp) cc_final: 0.5338 (mtt) REVERT: A 425 MET cc_start: 0.9158 (mmm) cc_final: 0.8849 (mmm) REVERT: A 432 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.5990 (t80) REVERT: K 115 MET cc_start: 0.7528 (tpt) cc_final: 0.7257 (ptt) REVERT: K 177 ASP cc_start: 0.7889 (t70) cc_final: 0.7554 (t70) REVERT: K 215 GLU cc_start: 0.5285 (OUTLIER) cc_final: 0.4745 (pm20) REVERT: K 245 MET cc_start: 0.8476 (mtm) cc_final: 0.7983 (mpp) REVERT: K 344 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8536 (mm-30) outliers start: 74 outliers final: 51 residues processed: 185 average time/residue: 0.1192 time to fit residues: 29.4423 Evaluate side-chains 168 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 106 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 344 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [28, 97, 58, 59, 4, 85, 70, 80, 88, 96, 8] chunk 28 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** 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 = 0.4171 r_free = 0.4171 target = 0.083217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.068666 restraints weight = 45177.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.070731 restraints weight = 25829.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.072109 restraints weight = 17048.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.073033 restraints weight = 12559.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.073676 restraints weight = 10064.065| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.9946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 9692 Z= 0.206 Angle : 0.855 16.771 13128 Z= 0.434 Chirality : 0.047 0.289 1461 Planarity : 0.007 0.099 1703 Dihedral : 9.628 77.717 1370 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.95 % Favored : 95.97 % Rotamer: Outliers : 6.21 % Allowed : 26.50 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.23), residues: 1191 helix: 0.29 (0.20), residues: 581 sheet: 0.11 (0.37), residues: 188 loop : -0.89 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 251 TYR 0.185 0.003 TYR A 224 PHE 0.036 0.003 PHE B 294 TRP 0.014 0.002 TRP B 21 HIS 0.014 0.002 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 ( 9681) covalent geometry : angle 0.85499 / 0.43 (13128) hydrogen bonds : bond 0.05607 / 3.96 ( 499) hydrogen bonds : angle 5.75485 / 4.35 ( 1551) Misc. bond : bond 0.01747 / 1.30 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 110 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.6130 (mm-30) REVERT: B 103 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7612 (mttt) REVERT: B 122 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8279 (mtmt) REVERT: B 216 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6834 (mtmm) REVERT: B 257 MET cc_start: 0.8927 (tpp) cc_final: 0.8527 (mmp) REVERT: B 270 PHE cc_start: 0.6854 (t80) cc_final: 0.6523 (t80) REVERT: B 293 MET cc_start: 0.7886 (mmt) cc_final: 0.6899 (ppp) REVERT: B 299 MET cc_start: 0.7252 (mmm) cc_final: 0.6996 (tpt) REVERT: B 415 MET cc_start: 0.8077 (tpp) cc_final: 0.7869 (mmp) REVERT: A 132 LEU cc_start: 0.7563 (mp) cc_final: 0.6906 (mt) REVERT: A 212 ILE cc_start: 0.8233 (mm) cc_final: 0.7948 (mm) REVERT: A 220 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5516 (pp20) REVERT: A 267 PHE cc_start: 0.6860 (OUTLIER) cc_final: 0.5828 (p90) REVERT: A 308 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6800 (mpt180) REVERT: A 313 MET cc_start: 0.6207 (mtp) cc_final: 0.5336 (mtt) REVERT: A 432 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.5928 (t80) REVERT: K 68 PHE cc_start: 0.7563 (m-10) cc_final: 0.7161 (m-10) REVERT: K 177 ASP cc_start: 0.7885 (t70) cc_final: 0.7544 (t70) REVERT: K 215 GLU cc_start: 0.5428 (OUTLIER) cc_final: 0.4891 (pm20) REVERT: K 239 PHE cc_start: 0.8598 (t80) cc_final: 0.8039 (t80) REVERT: K 245 MET cc_start: 0.8516 (mtm) cc_final: 0.8028 (mpp) REVERT: K 344 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8567 (mm-30) outliers start: 64 outliers final: 51 residues processed: 161 average time/residue: 0.1142 time to fit residues: 24.7344 Evaluate side-chains 168 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 107 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 344 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [6, 75, 5, 67, 36, 100, 55, 22, 116, 38, 91] chunk 6 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 195 ASN A 186 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** 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 = 0.4144 r_free = 0.4144 target = 0.082087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.067548 restraints weight = 45544.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.069545 restraints weight = 26011.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.070907 restraints weight = 17225.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.071808 restraints weight = 12733.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.072393 restraints weight = 10231.466| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 1.0234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 9692 Z= 0.219 Angle : 0.847 16.982 13128 Z= 0.434 Chirality : 0.046 0.272 1461 Planarity : 0.009 0.250 1703 Dihedral : 9.626 75.660 1370 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 26.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 6.60 % Allowed : 25.83 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.23), residues: 1191 helix: 0.27 (0.20), residues: 585 sheet: 0.14 (0.38), residues: 186 loop : -0.98 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 251 TYR 0.168 0.003 TYR A 224 PHE 0.042 0.003 PHE B 378 TRP 0.012 0.002 TRP B 21 HIS 0.022 0.003 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 ( 9681) covalent geometry : angle 0.84679 / 0.43 (13128) hydrogen bonds : bond 0.05742 / 4.08 ( 499) hydrogen bonds : angle 5.70650 / 4.33 ( 1551) Misc. bond : bond 0.01688 / 1.22 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 111 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7584 (mttt) REVERT: B 122 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8270 (mtmt) REVERT: B 191 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.7176 (pp30) REVERT: B 216 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6718 (mtmm) REVERT: B 257 MET cc_start: 0.8984 (tpp) cc_final: 0.8735 (mmm) REVERT: B 270 PHE cc_start: 0.7177 (t80) cc_final: 0.6825 (t80) REVERT: B 293 MET cc_start: 0.7808 (mmt) cc_final: 0.6974 (ppp) REVERT: B 299 MET cc_start: 0.7265 (mmm) cc_final: 0.6982 (tpt) REVERT: A 132 LEU cc_start: 0.7817 (mp) cc_final: 0.7264 (mt) REVERT: A 212 ILE cc_start: 0.8254 (mm) cc_final: 0.7985 (mm) REVERT: A 220 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.5451 (pp20) REVERT: A 267 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.5841 (p90) REVERT: A 308 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7010 (mpt180) REVERT: A 313 MET cc_start: 0.6346 (mtp) cc_final: 0.5476 (mtt) REVERT: A 425 MET cc_start: 0.9094 (mmm) cc_final: 0.8763 (mmm) REVERT: A 432 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.5998 (t80) REVERT: K 68 PHE cc_start: 0.7645 (m-10) cc_final: 0.7269 (m-10) REVERT: K 177 ASP cc_start: 0.7916 (t70) cc_final: 0.7577 (t70) REVERT: K 215 GLU cc_start: 0.5509 (OUTLIER) cc_final: 0.4991 (pm20) REVERT: K 239 PHE cc_start: 0.8658 (t80) cc_final: 0.8129 (t80) REVERT: K 245 MET cc_start: 0.8483 (mtm) cc_final: 0.8009 (mpp) REVERT: K 344 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8575 (mm-30) outliers start: 68 outliers final: 52 residues processed: 166 average time/residue: 0.1112 time to fit residues: 24.7362 Evaluate side-chains 165 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 103 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 344 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [97, 111, 99, 90, 98, 87, 27, 13, 117, 61, 71] chunk 97 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 71 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN A 61 HIS A 186 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** A 372 GLN ** 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 = 0.4156 r_free = 0.4156 target = 0.082642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.068111 restraints weight = 45285.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.070141 restraints weight = 25725.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.071504 restraints weight = 16988.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.072396 restraints weight = 12533.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.072967 restraints weight = 10103.477| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 1.0515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9692 Z= 0.202 Angle : 0.875 20.117 13128 Z= 0.441 Chirality : 0.047 0.270 1461 Planarity : 0.011 0.336 1703 Dihedral : 9.576 76.599 1370 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 26.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 5.73 % Allowed : 26.89 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.23), residues: 1191 helix: 0.35 (0.20), residues: 583 sheet: 0.13 (0.38), residues: 189 loop : -1.01 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 251 TYR 0.201 0.003 TYR A 224 PHE 0.041 0.003 PHE K 72 TRP 0.012 0.002 TRP B 101 HIS 0.016 0.002 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 9681) covalent geometry : angle 0.87502 / 0.44 (13128) hydrogen bonds : bond 0.05583 / 3.96 ( 499) hydrogen bonds : angle 5.75884 / 4.37 ( 1551) Misc. bond : bond 0.01757 / 1.30 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 115 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7517 (mttt) REVERT: B 122 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8286 (mtmt) REVERT: B 257 MET cc_start: 0.8975 (tpp) cc_final: 0.8588 (mmp) REVERT: B 270 PHE cc_start: 0.7048 (t80) cc_final: 0.6803 (t80) REVERT: B 293 MET cc_start: 0.7899 (mmt) cc_final: 0.7150 (ppp) REVERT: B 299 MET cc_start: 0.7172 (mmm) cc_final: 0.6869 (tpt) REVERT: A 132 LEU cc_start: 0.7800 (mp) cc_final: 0.7341 (mt) REVERT: A 212 ILE cc_start: 0.8271 (mm) cc_final: 0.7974 (mm) REVERT: A 220 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5560 (pp20) REVERT: A 267 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.5928 (p90) REVERT: A 308 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7155 (mpt180) REVERT: A 313 MET cc_start: 0.6326 (mtp) cc_final: 0.5490 (mtt) REVERT: A 432 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6000 (t80) REVERT: K 68 PHE cc_start: 0.7631 (m-10) cc_final: 0.7234 (m-10) REVERT: K 115 MET cc_start: 0.8071 (tpp) cc_final: 0.7821 (ptt) REVERT: K 177 ASP cc_start: 0.7844 (t70) cc_final: 0.7510 (t70) REVERT: K 215 GLU cc_start: 0.5582 (OUTLIER) cc_final: 0.5081 (pm20) REVERT: K 239 PHE cc_start: 0.8659 (t80) cc_final: 0.8095 (t80) REVERT: K 245 MET cc_start: 0.8510 (mtm) cc_final: 0.8041 (mpp) REVERT: K 344 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8639 (mm-30) outliers start: 59 outliers final: 44 residues processed: 163 average time/residue: 0.1152 time to fit residues: 25.2146 Evaluate side-chains 159 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 107 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 344 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [41, 59, 69, 79, 11, 60, 93, 38, 97, 96, 48] chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 69 optimal weight: 0.0470 chunk 79 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** 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 = 0.4160 r_free = 0.4160 target = 0.082996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.068519 restraints weight = 45133.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.070520 restraints weight = 25675.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.071867 restraints weight = 17060.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.072733 restraints weight = 12618.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.073306 restraints weight = 10226.310| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 1.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 9692 Z= 0.207 Angle : 0.907 18.948 13128 Z= 0.453 Chirality : 0.047 0.262 1461 Planarity : 0.010 0.219 1703 Dihedral : 9.337 76.092 1364 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 24.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 5.63 % Allowed : 26.80 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.24), residues: 1191 helix: 0.37 (0.21), residues: 577 sheet: 0.14 (0.39), residues: 188 loop : -0.99 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.001 ARG B 251 TYR 0.189 0.003 TYR A 224 PHE 0.026 0.003 PHE A 53 TRP 0.011 0.002 TRP B 21 HIS 0.031 0.002 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 ( 9681) covalent geometry : angle 0.90666 / 0.45 (13128) hydrogen bonds : bond 0.05473 / 3.89 ( 499) hydrogen bonds : angle 5.71587 / 4.35 ( 1551) Misc. bond : bond 0.01774 / 1.29 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2174.66 seconds wall clock time: 38 minutes 28.70 seconds (2308.70 seconds total)