Starting phenix.real_space_refine on Fri Sep 11 14:04:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ta3_10421/09_2026/6ta3_10421.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ta3_10421/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6ta3_10421/09_2026/6ta3_10421.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ta3_10421/09_2026/6ta3_10421.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ta3_10421/09_2026/6ta3_10421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ta3_10421/09_2026/6ta3_10421.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ta3_10421/09_2026/6ta3_10421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ta3_10421/09_2026/6ta3_10421.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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-2.2.1-6174/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: 1.78, per 1000 atoms: 0.19 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 347.6 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: 0.29 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: 1.66 Time building geometry restraints manager: 1.53 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: 110 2.22 - 3.12: 13174 3.12 - 4.01: 31103 4.01 - 4.90: 53116 Warning: very small nonbonded interaction distances. Nonbonded interactions: 97517 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 97512 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: 11.340 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.320 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.280 ------------------------------------------------------------------------------- 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 : 0.032 1.113 9691 Z= 2.718 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 0.68362 / 32.62 ( 10) *********************** 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 : 0.277 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: 0.1379 time to fit residues: 60.1840 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 : 0.385 ------------------------------------------------------------------------------- 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: 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** B 347 ASN A 18 ASN A 31 GLN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.089521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.075093 restraints weight = 44356.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.077579 restraints weight = 24811.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.079233 restraints weight = 15873.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.080352 restraints weight = 11336.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.081044 restraints weight = 8827.017| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 9691 Z= 0.319 Angle : 1.060 16.256 13128 Z= 0.563 Chirality : 0.058 0.393 1461 Planarity : 0.010 0.116 1703 Dihedral : 14.713 87.866 1530 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 47.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 11.75 % Allowed : 20.97 % Favored : 67.28 % 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: -0.14 (0.22), residues: 1191 helix: 0.02 (0.19), residues: 571 sheet: 1.14 (0.37), residues: 184 loop : -0.62 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 181 TYR 0.144 0.004 TYR A 224 PHE 0.039 0.004 PHE B 385 TRP 0.012 0.003 TRP A 407 HIS 0.014 0.003 HIS A 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.32 ( 9681) covalent geometry : angle 1.05955 / 0.56 (13128) hydrogen bonds : bond 0.08235 / 5.75 ( 499) hydrogen bonds : angle 7.03640 / 5.31 ( 1551) Misc. bond : bond 0.01527 / 0.99 ( 10) *********************** 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 284 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 163 time to evaluate : 0.375 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: B 3 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.6194 (mm-30) REVERT: B 22 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6908 (pp20) REVERT: B 23 VAL cc_start: 0.8701 (p) cc_final: 0.8089 (m) REVERT: B 31 ASP cc_start: 0.3269 (OUTLIER) cc_final: 0.2978 (t0) REVERT: B 122 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7851 (mtmt) REVERT: B 147 MET cc_start: 0.7297 (pmm) cc_final: 0.6819 (pmm) REVERT: B 154 LYS cc_start: 0.9250 (mmmt) cc_final: 0.8695 (tttp) REVERT: B 155 ILE cc_start: 0.7526 (pt) cc_final: 0.7254 (tp) REVERT: B 158 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.5836 (mp0) REVERT: B 228 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8282 (tt) REVERT: B 280 GLN cc_start: 0.7245 (pt0) cc_final: 0.6975 (pt0) REVERT: B 291 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8389 (pp30) REVERT: B 336 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8163 (mttt) REVERT: B 363 MET cc_start: 0.8121 (mpp) cc_final: 0.7910 (mpp) REVERT: A 40 LYS cc_start: 0.6718 (OUTLIER) cc_final: 0.6423 (mmtp) REVERT: A 52 PHE cc_start: 0.6250 (m-10) cc_final: 0.5582 (m-10) REVERT: A 149 PHE cc_start: 0.6965 (t80) cc_final: 0.6738 (t80) REVERT: A 164 LYS cc_start: 0.5176 (OUTLIER) cc_final: 0.4707 (tppt) REVERT: A 212 ILE cc_start: 0.8093 (mm) cc_final: 0.7751 (mm) REVERT: A 220 GLU cc_start: 0.4792 (OUTLIER) cc_final: 0.3430 (pp20) REVERT: A 242 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5519 (tm) REVERT: A 338 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8060 (tppp) REVERT: A 371 VAL cc_start: 0.3900 (OUTLIER) cc_final: 0.3673 (t) REVERT: A 404 PHE cc_start: 0.7159 (m-10) cc_final: 0.6749 (m-80) REVERT: K 101 ILE cc_start: 0.9230 (mt) cc_final: 0.8988 (tp) REVERT: K 157 LYS cc_start: 0.7620 (mttt) cc_final: 0.7398 (ptmm) REVERT: K 177 ASP cc_start: 0.7718 (t70) cc_final: 0.7358 (t70) REVERT: K 184 MET cc_start: 0.7052 (tmm) cc_final: 0.6780 (tmm) REVERT: K 203 THR cc_start: 0.5677 (OUTLIER) cc_final: 0.4761 (m) REVERT: K 261 LEU cc_start: 0.9332 (tp) cc_final: 0.9042 (tp) REVERT: K 263 LEU cc_start: 0.8850 (mm) cc_final: 0.8295 (mt) REVERT: K 290 GLN cc_start: 0.8808 (pp30) cc_final: 0.8243 (pt0) outliers start: 121 outliers final: 50 residues processed: 255 average time/residue: 0.1209 time to fit residues: 40.6959 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 : 0.281 ------------------------------------------------------------------------------- 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 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 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 334 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain A residue 40 LYS 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 135 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 164 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 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 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 203 THR 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 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: chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 0.0040 chunk 95 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** 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 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.085649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.070803 restraints weight = 45143.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.072990 restraints weight = 25577.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.074428 restraints weight = 16773.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.075402 restraints weight = 12308.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.076076 restraints weight = 9828.296| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.7158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9691 Z= 0.256 Angle : 0.908 16.340 13128 Z= 0.477 Chirality : 0.051 0.338 1461 Planarity : 0.008 0.092 1703 Dihedral : 12.166 79.509 1440 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 37.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.27 % Favored : 97.65 % Rotamer: Outliers : 9.51 % Allowed : 22.62 % Favored : 67.86 % 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: -0.26 (0.23), residues: 1191 helix: 0.09 (0.20), residues: 563 sheet: 0.58 (0.36), residues: 190 loop : -0.69 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 221 TYR 0.146 0.003 TYR A 224 PHE 0.028 0.003 PHE B 385 TRP 0.034 0.003 TRP B 101 HIS 0.011 0.002 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 ( 9681) covalent geometry : angle 0.90766 / 0.48 (13128) hydrogen bonds : bond 0.06999 / 4.92 ( 499) hydrogen bonds : angle 6.48139 / 4.95 ( 1551) Misc. bond : bond 0.01504 / 0.98 ( 10) *********************** 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 231 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 133 time to evaluate : 0.373 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 122 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8146 (mtmt) REVERT: B 155 ILE cc_start: 0.8106 (pt) cc_final: 0.7783 (mm) REVERT: B 156 ARG cc_start: 0.7949 (tpt90) cc_final: 0.7161 (tpp80) REVERT: B 233 MET cc_start: 0.6705 (mtp) cc_final: 0.6029 (tpp) REVERT: B 293 MET cc_start: 0.7579 (mmt) cc_final: 0.6485 (ppp) REVERT: B 331 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8092 (pp) REVERT: B 336 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8104 (mttt) REVERT: B 379 LYS cc_start: 0.8563 (pttp) cc_final: 0.8350 (pttp) REVERT: A 52 PHE cc_start: 0.6186 (m-10) cc_final: 0.5812 (m-10) REVERT: A 209 ILE cc_start: 0.7471 (mt) cc_final: 0.7051 (mt) REVERT: A 212 ILE cc_start: 0.8207 (mm) cc_final: 0.7875 (mm) REVERT: A 242 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5439 (tm) REVERT: A 267 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.5833 (p90) REVERT: A 313 MET cc_start: 0.6023 (mtp) cc_final: 0.5204 (mtt) REVERT: A 432 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.5995 (t80) REVERT: K 177 ASP cc_start: 0.7913 (t70) cc_final: 0.7588 (t70) REVERT: K 261 LEU cc_start: 0.9388 (tp) cc_final: 0.9184 (tp) REVERT: K 290 GLN cc_start: 0.8880 (pp30) cc_final: 0.8358 (pt0) REVERT: K 304 GLU cc_start: 0.7950 (tp30) cc_final: 0.7720 (tm-30) REVERT: K 367 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.5920 (tp-100) outliers start: 98 outliers final: 53 residues processed: 203 average time/residue: 0.1184 time to fit residues: 32.0311 Evaluate side-chains 168 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 108 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 72 THR 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 189 VAL 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 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 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 407 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 ARG 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 150 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 179 THR 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 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 233 GLN 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 28 PHE Chi-restraints excluded: chain K residue 34 LYS 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 302 LEU 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: chunk 77 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.085384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.070647 restraints weight = 45218.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.072834 restraints weight = 25399.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.074245 restraints weight = 16651.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.075217 restraints weight = 12200.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.075852 restraints weight = 9770.373| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.7976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9691 Z= 0.215 Angle : 0.878 19.398 13128 Z= 0.454 Chirality : 0.047 0.202 1461 Planarity : 0.008 0.156 1703 Dihedral : 11.087 90.512 1398 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 32.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 7.86 % Allowed : 25.44 % Favored : 66.70 % 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: -0.34 (0.23), residues: 1191 helix: 0.11 (0.20), residues: 562 sheet: 0.36 (0.36), residues: 189 loop : -0.78 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 33 TYR 0.141 0.003 TYR A 224 PHE 0.024 0.003 PHE B 385 TRP 0.016 0.002 TRP A 388 HIS 0.018 0.002 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 ( 9681) covalent geometry : angle 0.87793 / 0.45 (13128) hydrogen bonds : bond 0.06377 / 4.48 ( 499) hydrogen bonds : angle 6.17917 / 4.67 ( 1551) Misc. bond : bond 0.01569 / 1.00 ( 10) *********************** 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 209 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 128 time to evaluate : 0.434 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: B 103 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7562 (mttt) REVERT: B 114 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8089 (t0) REVERT: B 122 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8021 (mtmt) REVERT: B 270 PHE cc_start: 0.6951 (t80) cc_final: 0.6520 (t80) REVERT: B 286 VAL cc_start: 0.7605 (OUTLIER) cc_final: 0.7340 (t) REVERT: B 293 MET cc_start: 0.7642 (mmt) cc_final: 0.6365 (ppp) REVERT: B 336 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8315 (mttt) REVERT: B 378 PHE cc_start: 0.8166 (m-10) cc_final: 0.7964 (m-10) REVERT: A 52 PHE cc_start: 0.5989 (m-10) cc_final: 0.5494 (m-10) REVERT: A 209 ILE cc_start: 0.7666 (mt) cc_final: 0.7457 (mt) REVERT: A 212 ILE cc_start: 0.8257 (mm) cc_final: 0.7951 (mm) REVERT: A 242 LEU cc_start: 0.5522 (OUTLIER) cc_final: 0.5206 (tm) REVERT: A 267 PHE cc_start: 0.6457 (OUTLIER) cc_final: 0.5471 (p90) REVERT: A 311 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6682 (mppt) REVERT: A 313 MET cc_start: 0.6036 (mtp) cc_final: 0.5420 (mtt) REVERT: A 425 MET cc_start: 0.9242 (mmm) cc_final: 0.8932 (mmm) REVERT: A 432 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.5965 (t80) REVERT: K 177 ASP cc_start: 0.7849 (t70) cc_final: 0.7518 (t70) REVERT: K 181 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.6019 (tmt170) REVERT: K 211 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7622 (t80) REVERT: K 245 MET cc_start: 0.8299 (mtm) cc_final: 0.7876 (mpp) REVERT: K 367 GLN cc_start: 0.6668 (OUTLIER) cc_final: 0.5676 (tm-30) outliers start: 81 outliers final: 40 residues processed: 191 average time/residue: 0.1112 time to fit residues: 28.9245 Evaluate side-chains 164 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 112 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 72 THR 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 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 286 VAL 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 359 ARG Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG 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 179 THR 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 233 GLN 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 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 34 LYS 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 211 TYR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 237 SER Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 272 ILE 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: chunk 46 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 HIS B 8 GLN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 226 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 264 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** 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 233 GLN ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 173 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.081594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.066945 restraints weight = 45912.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.068993 restraints weight = 25994.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.070350 restraints weight = 17035.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.071278 restraints weight = 12506.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.071913 restraints weight = 10006.505| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.8838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 9691 Z= 0.266 Angle : 0.874 15.966 13128 Z= 0.466 Chirality : 0.049 0.261 1461 Planarity : 0.008 0.095 1703 Dihedral : 10.535 98.725 1388 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 32.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 8.54 % Allowed : 23.50 % Favored : 67.96 % 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: -0.44 (0.23), residues: 1191 helix: 0.18 (0.20), residues: 566 sheet: -0.03 (0.36), residues: 189 loop : -0.88 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.052 0.001 ARG B 251 TYR 0.143 0.003 TYR A 224 PHE 0.030 0.003 PHE B 260 TRP 0.029 0.003 TRP B 21 HIS 0.017 0.003 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.26 ( 9681) covalent geometry : angle 0.87351 / 0.47 (13128) hydrogen bonds : bond 0.06577 / 4.59 ( 499) hydrogen bonds : angle 6.15095 / 4.65 ( 1551) Misc. bond : bond 0.01596 / 1.01 ( 10) *********************** 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 203 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 115 time to evaluate : 0.372 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: B 114 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8139 (t0) REVERT: B 122 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8267 (mtmt) REVERT: B 147 MET cc_start: 0.7344 (pmm) cc_final: 0.6761 (pmm) REVERT: B 256 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.7273 (t0) REVERT: B 270 PHE cc_start: 0.7034 (t80) cc_final: 0.6608 (t80) REVERT: B 299 MET cc_start: 0.7961 (mmt) cc_final: 0.7593 (tpp) REVERT: B 336 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8276 (mttt) REVERT: B 378 PHE cc_start: 0.8210 (m-10) cc_final: 0.7994 (m-10) REVERT: A 40 LYS cc_start: 0.6569 (OUTLIER) cc_final: 0.5801 (mmmm) REVERT: A 176 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.7012 (pt0) REVERT: A 188 ILE cc_start: 0.7386 (mp) cc_final: 0.7163 (mt) REVERT: A 212 ILE cc_start: 0.8299 (mm) cc_final: 0.7976 (mm) REVERT: A 220 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.6020 (pp20) REVERT: A 267 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.5693 (p90) REVERT: A 313 MET cc_start: 0.6483 (mtp) cc_final: 0.5733 (mtt) REVERT: A 373 ARG cc_start: 0.7448 (mpt180) cc_final: 0.6836 (mtt180) REVERT: A 432 TYR cc_start: 0.7196 (OUTLIER) cc_final: 0.5996 (t80) REVERT: K 70 MET cc_start: 0.8339 (tpp) cc_final: 0.8096 (tpp) REVERT: K 177 ASP cc_start: 0.7880 (t70) cc_final: 0.7525 (t70) REVERT: K 239 PHE cc_start: 0.8626 (t80) cc_final: 0.8055 (t80) REVERT: K 245 MET cc_start: 0.8350 (mtm) cc_final: 0.7871 (mpp) REVERT: K 367 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.5925 (tm-30) outliers start: 88 outliers final: 54 residues processed: 181 average time/residue: 0.1081 time to fit residues: 26.7153 Evaluate side-chains 169 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 105 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 72 THR 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 155 ILE Chi-restraints excluded: chain B residue 170 VAL 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 256 ASN 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 326 VAL Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 40 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 176 GLN Chi-restraints excluded: chain A residue 179 THR 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 217 LEU 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 239 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 311 LYS 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 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 248 THR Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE 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: chunk 10 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 335 ASN ** 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 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.080966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.066388 restraints weight = 44311.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.068387 restraints weight = 25199.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.069730 restraints weight = 16587.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.070638 restraints weight = 12168.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.071230 restraints weight = 9753.393| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.9296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9691 Z= 0.239 Angle : 0.842 15.806 13128 Z= 0.443 Chirality : 0.048 0.358 1461 Planarity : 0.008 0.095 1703 Dihedral : 10.110 98.772 1374 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 30.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 7.28 % Allowed : 25.05 % 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: -0.50 (0.23), residues: 1191 helix: 0.13 (0.20), residues: 570 sheet: -0.19 (0.37), residues: 188 loop : -0.84 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 251 TYR 0.142 0.003 TYR A 224 PHE 0.049 0.003 PHE B 167 TRP 0.020 0.002 TRP B 21 HIS 0.016 0.002 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 ( 9681) covalent geometry : angle 0.84216 / 0.44 (13128) hydrogen bonds : bond 0.06372 / 4.47 ( 499) hydrogen bonds : angle 5.95474 / 4.53 ( 1551) Misc. bond : bond 0.01602 / 1.01 ( 10) *********************** 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 190 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 115 time to evaluate : 0.405 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: B 114 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8228 (t0) REVERT: B 122 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8322 (mtmt) REVERT: B 147 MET cc_start: 0.7420 (pmm) cc_final: 0.6982 (pmm) REVERT: B 252 LYS cc_start: 0.6269 (OUTLIER) cc_final: 0.5929 (mtmt) REVERT: B 270 PHE cc_start: 0.6903 (t80) cc_final: 0.6593 (t80) REVERT: B 336 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8372 (mttp) REVERT: B 415 MET cc_start: 0.6689 (tmm) cc_final: 0.6349 (tmm) REVERT: A 40 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6044 (mmmm) REVERT: A 212 ILE cc_start: 0.8366 (mm) cc_final: 0.8061 (mm) REVERT: A 214 ARG cc_start: 0.7004 (tmm160) cc_final: 0.6554 (tmm160) REVERT: A 220 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5762 (pp20) REVERT: A 242 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.4616 (tt) REVERT: A 267 PHE cc_start: 0.6698 (OUTLIER) cc_final: 0.5663 (p90) REVERT: A 311 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6739 (mppt) REVERT: A 313 MET cc_start: 0.6649 (mtp) cc_final: 0.5810 (mtt) REVERT: A 373 ARG cc_start: 0.7745 (mpt180) cc_final: 0.7142 (mtt180) REVERT: A 432 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.5992 (t80) REVERT: K 70 MET cc_start: 0.8307 (tpp) cc_final: 0.8034 (tpp) REVERT: K 115 MET cc_start: 0.7213 (tpt) cc_final: 0.6973 (ptt) REVERT: K 177 ASP cc_start: 0.7934 (t70) cc_final: 0.7582 (t70) REVERT: K 239 PHE cc_start: 0.8796 (t80) cc_final: 0.8476 (t80) REVERT: K 245 MET cc_start: 0.8460 (mtm) cc_final: 0.7898 (mpp) REVERT: K 367 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.5880 (tm-30) outliers start: 75 outliers final: 49 residues processed: 173 average time/residue: 0.1090 time to fit residues: 26.0215 Evaluate side-chains 162 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 102 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 72 THR 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 170 VAL Chi-restraints excluded: chain B residue 190 HIS 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 276 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain A residue 40 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 179 THR 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 239 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 311 LYS 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 367 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** 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 342 GLN ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.080834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.066144 restraints weight = 45183.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.068105 restraints weight = 25881.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.069446 restraints weight = 17136.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.070338 restraints weight = 12597.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.070838 restraints weight = 10164.108| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.9721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9691 Z= 0.221 Angle : 0.845 15.121 13128 Z= 0.438 Chirality : 0.048 0.274 1461 Planarity : 0.009 0.203 1703 Dihedral : 9.555 59.474 1371 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 29.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 7.48 % Allowed : 25.24 % 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: -0.44 (0.23), residues: 1191 helix: 0.24 (0.20), residues: 567 sheet: -0.19 (0.38), residues: 186 loop : -0.88 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 33 TYR 0.182 0.003 TYR A 224 PHE 0.035 0.003 PHE B 167 TRP 0.015 0.002 TRP B 21 HIS 0.018 0.002 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 ( 9681) covalent geometry : angle 0.84545 / 0.44 (13128) hydrogen bonds : bond 0.06139 / 4.33 ( 499) hydrogen bonds : angle 5.83890 / 4.44 ( 1551) Misc. bond : bond 0.01758 / 1.14 ( 10) *********************** 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 186 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 109 time to evaluate : 0.341 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 114 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8136 (t0) REVERT: B 122 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8280 (mtmt) REVERT: B 252 LYS cc_start: 0.5677 (OUTLIER) cc_final: 0.5278 (ptmt) REVERT: B 270 PHE cc_start: 0.7095 (t80) cc_final: 0.6791 (t80) REVERT: B 336 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8269 (mtmm) REVERT: A 40 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6411 (mmmm) REVERT: A 52 PHE cc_start: 0.5917 (m-10) cc_final: 0.5639 (m-80) REVERT: A 212 ILE cc_start: 0.8343 (mm) cc_final: 0.8039 (mm) REVERT: A 220 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5928 (pp20) REVERT: A 242 LEU cc_start: 0.5401 (OUTLIER) cc_final: 0.5174 (tm) REVERT: A 267 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.5502 (p90) REVERT: A 311 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6752 (mppt) REVERT: A 313 MET cc_start: 0.6653 (mtp) cc_final: 0.5927 (mtt) REVERT: A 373 ARG cc_start: 0.7778 (mpt180) cc_final: 0.7206 (mtt180) REVERT: A 396 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8136 (t0) REVERT: A 432 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.6101 (t80) REVERT: K 70 MET cc_start: 0.8361 (tpp) cc_final: 0.8145 (tpp) REVERT: K 115 MET cc_start: 0.7478 (tpt) cc_final: 0.7277 (ptt) REVERT: K 177 ASP cc_start: 0.7897 (t70) cc_final: 0.7551 (t70) REVERT: K 239 PHE cc_start: 0.8826 (t80) cc_final: 0.8414 (t80) outliers start: 77 outliers final: 52 residues processed: 170 average time/residue: 0.1108 time to fit residues: 25.5886 Evaluate side-chains 163 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 100 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 72 THR 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 130 LEU Chi-restraints excluded: chain B residue 155 ILE 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 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 276 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS 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 359 ARG Chi-restraints excluded: chain A residue 40 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 179 THR 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 239 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 311 LYS 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 396 ASP 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 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 248 THR Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 88 optimal weight: 0.0470 chunk 96 optimal weight: 1.9990 chunk 8 optimal weight: 0.0000 overall best weight: 0.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.081408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.066855 restraints weight = 45435.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.068834 restraints weight = 25905.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.070162 restraints weight = 17119.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.071048 restraints weight = 12643.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.071620 restraints weight = 10193.558| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 1.0108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9691 Z= 0.200 Angle : 0.868 21.446 13128 Z= 0.436 Chirality : 0.047 0.265 1461 Planarity : 0.010 0.236 1703 Dihedral : 9.396 59.044 1371 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 27.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.31 % Allowed : 26.41 % 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: -0.34 (0.23), residues: 1191 helix: 0.29 (0.20), residues: 570 sheet: -0.07 (0.38), residues: 192 loop : -0.83 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 251 TYR 0.187 0.003 TYR A 224 PHE 0.032 0.003 PHE B 260 TRP 0.017 0.002 TRP B 21 HIS 0.013 0.002 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 9681) covalent geometry : angle 0.86822 / 0.44 (13128) hydrogen bonds : bond 0.05874 / 4.14 ( 499) hydrogen bonds : angle 5.74462 / 4.38 ( 1551) Misc. bond : bond 0.01656 / 1.06 ( 10) *********************** 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 178 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 113 time to evaluate : 0.390 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 122 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8253 (mtmt) REVERT: B 252 LYS cc_start: 0.5458 (OUTLIER) cc_final: 0.5247 (ptmt) REVERT: B 257 MET cc_start: 0.9151 (tpp) cc_final: 0.8518 (mmt) REVERT: B 270 PHE cc_start: 0.6923 (t80) cc_final: 0.6563 (t80) REVERT: B 293 MET cc_start: 0.7582 (mmp) cc_final: 0.6863 (tmm) REVERT: A 40 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.6374 (mmmm) REVERT: A 52 PHE cc_start: 0.5964 (m-10) cc_final: 0.5737 (m-80) REVERT: A 212 ILE cc_start: 0.8252 (mm) cc_final: 0.7957 (mm) REVERT: A 220 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5744 (pp20) REVERT: A 267 PHE cc_start: 0.6409 (OUTLIER) cc_final: 0.5397 (p90) REVERT: A 286 LEU cc_start: 0.7178 (pp) cc_final: 0.6737 (pp) REVERT: A 313 MET cc_start: 0.6636 (mtp) cc_final: 0.5835 (mtt) REVERT: A 373 ARG cc_start: 0.7724 (mpt180) cc_final: 0.7315 (mtt180) REVERT: A 432 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6057 (t80) REVERT: K 70 MET cc_start: 0.8392 (tpp) cc_final: 0.8152 (tpp) REVERT: K 115 MET cc_start: 0.7576 (tpt) cc_final: 0.7362 (ptt) REVERT: K 177 ASP cc_start: 0.7846 (t70) cc_final: 0.7530 (t70) REVERT: K 239 PHE cc_start: 0.8892 (t80) cc_final: 0.8417 (t80) REVERT: K 245 MET cc_start: 0.8542 (mtm) cc_final: 0.8111 (mpp) outliers start: 65 outliers final: 54 residues processed: 163 average time/residue: 0.1130 time to fit residues: 25.1536 Evaluate side-chains 162 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 102 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 49 VAL Chi-restraints excluded: chain B residue 72 THR 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 130 LEU Chi-restraints excluded: chain B residue 155 ILE 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 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 276 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS 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 388 MET Chi-restraints excluded: chain A residue 40 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 179 THR 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 255 PHE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 367 ASP 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 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 248 THR Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.077913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.063508 restraints weight = 46409.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.065368 restraints weight = 26695.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.066594 restraints weight = 17858.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.067358 restraints weight = 13340.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.067944 restraints weight = 10957.103| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 1.0526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 9691 Z= 0.289 Angle : 0.943 17.852 13128 Z= 0.488 Chirality : 0.050 0.271 1461 Planarity : 0.013 0.384 1703 Dihedral : 9.591 59.994 1367 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 33.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 6.50 % Allowed : 27.09 % Favored : 66.41 % 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: -0.68 (0.23), residues: 1191 helix: 0.09 (0.20), residues: 572 sheet: -0.09 (0.39), residues: 177 loop : -1.19 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 221 TYR 0.180 0.004 TYR A 224 PHE 0.037 0.003 PHE B 270 TRP 0.013 0.003 TRP B 21 HIS 0.019 0.003 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.28 ( 9681) covalent geometry : angle 0.94325 / 0.49 (13128) hydrogen bonds : bond 0.06785 / 4.78 ( 499) hydrogen bonds : angle 5.97329 / 4.54 ( 1551) Misc. bond : bond 0.01715 / 1.10 ( 10) *********************** 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 171 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 104 time to evaluate : 0.363 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 114 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8213 (t0) REVERT: B 122 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8238 (mtmt) REVERT: B 252 LYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5513 (ptmt) REVERT: B 257 MET cc_start: 0.9201 (tpp) cc_final: 0.8637 (mmt) REVERT: B 293 MET cc_start: 0.7679 (mmp) cc_final: 0.7075 (tmm) REVERT: B 415 MET cc_start: 0.8248 (tpp) cc_final: 0.8004 (mmp) REVERT: A 40 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6048 (mmtp) REVERT: A 212 ILE cc_start: 0.8249 (mm) cc_final: 0.7896 (mm) REVERT: A 220 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5861 (pp20) REVERT: A 267 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.5774 (p90) REVERT: A 313 MET cc_start: 0.6928 (mtp) cc_final: 0.6085 (mtt) REVERT: A 396 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8104 (t0) REVERT: A 432 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6135 (t80) REVERT: K 115 MET cc_start: 0.7570 (tpt) cc_final: 0.7363 (ptt) REVERT: K 177 ASP cc_start: 0.7881 (t70) cc_final: 0.7570 (t70) REVERT: K 239 PHE cc_start: 0.8816 (t80) cc_final: 0.7982 (t80) REVERT: K 245 MET cc_start: 0.8344 (mtm) cc_final: 0.7916 (mpp) outliers start: 67 outliers final: 56 residues processed: 154 average time/residue: 0.1114 time to fit residues: 23.5007 Evaluate side-chains 156 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 92 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 72 THR 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 130 LEU Chi-restraints excluded: chain B residue 155 ILE 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 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 252 LYS 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 326 VAL Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain A residue 40 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 179 THR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 193 THR 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 239 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 396 ASP 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 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 248 THR Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 99 optimal weight: 0.0570 chunk 90 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 61 optimal weight: 0.0870 chunk 71 optimal weight: 0.0870 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN K 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.081844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.067096 restraints weight = 45781.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.069097 restraints weight = 26312.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.070395 restraints weight = 17527.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.071252 restraints weight = 13083.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.071840 restraints weight = 10652.631| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 1.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9691 Z= 0.197 Angle : 0.896 17.909 13128 Z= 0.456 Chirality : 0.048 0.308 1461 Planarity : 0.007 0.101 1703 Dihedral : 9.108 57.471 1363 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 26.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.47 % Rotamer: Outliers : 4.76 % Allowed : 28.35 % Favored : 66.89 % 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: -0.44 (0.24), residues: 1191 helix: 0.23 (0.21), residues: 571 sheet: 0.06 (0.39), residues: 181 loop : -1.00 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.052 0.001 ARG B 251 TYR 0.173 0.003 TYR A 224 PHE 0.028 0.002 PHE B 260 TRP 0.023 0.002 TRP B 21 HIS 0.035 0.003 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 ( 9681) covalent geometry : angle 0.89619 / 0.46 (13128) hydrogen bonds : bond 0.05810 / 4.12 ( 499) hydrogen bonds : angle 5.74867 / 4.38 ( 1551) Misc. bond : bond 0.01746 / 1.11 ( 10) ********************** 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 160 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 111 time to evaluate : 0.440 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 122 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8294 (mtmt) REVERT: B 257 MET cc_start: 0.9019 (tpp) cc_final: 0.8615 (mmt) REVERT: B 293 MET cc_start: 0.7610 (mmp) cc_final: 0.7216 (tmm) REVERT: A 40 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6587 (mmmm) REVERT: A 212 ILE cc_start: 0.8183 (mm) cc_final: 0.7879 (mm) REVERT: A 220 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.5753 (pp20) REVERT: A 267 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.5752 (p90) REVERT: A 313 MET cc_start: 0.6853 (mtp) cc_final: 0.6030 (mtt) REVERT: A 373 ARG cc_start: 0.7746 (mpt180) cc_final: 0.7247 (mtt180) REVERT: A 432 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6095 (t80) REVERT: K 70 MET cc_start: 0.8182 (tpp) cc_final: 0.7911 (tpp) REVERT: K 177 ASP cc_start: 0.7758 (t70) cc_final: 0.7448 (t70) REVERT: K 239 PHE cc_start: 0.8684 (t80) cc_final: 0.8396 (t80) REVERT: K 245 MET cc_start: 0.8464 (mtm) cc_final: 0.8038 (mpp) REVERT: K 304 GLU cc_start: 0.8909 (tp30) cc_final: 0.8551 (tm-30) outliers start: 49 outliers final: 39 residues processed: 148 average time/residue: 0.1190 time to fit residues: 23.7648 Evaluate side-chains 143 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 HIS 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 130 LEU 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 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 A residue 40 LYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG 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 179 THR Chi-restraints excluded: chain A residue 193 THR 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 255 PHE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR 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 215 GLU Chi-restraints excluded: chain K residue 237 SER Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 0.0980 chunk 69 optimal weight: 0.0370 chunk 79 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 28 HIS ** 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 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.082131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.067453 restraints weight = 45303.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.069447 restraints weight = 26044.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.070755 restraints weight = 17300.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.071635 restraints weight = 12867.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.072210 restraints weight = 10423.220| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 1.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9691 Z= 0.192 Angle : 0.878 17.354 13128 Z= 0.444 Chirality : 0.048 0.307 1461 Planarity : 0.009 0.237 1703 Dihedral : 8.696 55.905 1357 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 26.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.20 % Favored : 95.72 % Rotamer: Outliers : 4.85 % Allowed : 28.45 % Favored : 66.70 % 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: -0.35 (0.24), residues: 1191 helix: 0.28 (0.21), residues: 573 sheet: -0.09 (0.38), residues: 193 loop : -0.83 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG B 251 TYR 0.167 0.003 TYR A 224 PHE 0.040 0.003 PHE A 52 TRP 0.011 0.002 TRP B 344 HIS 0.031 0.003 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 9681) covalent geometry : angle 0.87799 / 0.44 (13128) hydrogen bonds : bond 0.05691 / 4.04 ( 499) hydrogen bonds : angle 5.71802 / 4.35 ( 1551) Misc. bond : bond 0.01730 / 1.09 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.07 seconds wall clock time: 39 minutes 50.36 seconds (2390.36 seconds total)