Starting phenix.real_space_refine on Fri Mar 14 07:48:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ta3_10421/03_2025/6ta3_10421.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ta3_10421/03_2025/6ta3_10421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ta3_10421/03_2025/6ta3_10421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ta3_10421/03_2025/6ta3_10421.map" model { file = "/net/cci-nas-00/data/ceres_data/6ta3_10421/03_2025/6ta3_10421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ta3_10421/03_2025/6ta3_10421.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 8.19, per 1000 atoms: 0.86 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: 4.07 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.13 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: 3.40 Time building geometry restraints manager: 4.39 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: 5060 18.36 - 36.72: 507 36.72 - 55.08: 182 55.08 - 73.44: 86 73.44 - 91.80: 15 Dihedral angle restraints: 5850 sinusoidal: 2385 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 5847 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: 9.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.320 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5093 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 : 0.024 0.739 9681 Z= 1.609 Angle : 2.453 33.803 13128 Z= 1.751 Chirality : 0.078 0.913 1461 Planarity : 0.013 0.190 1703 Dihedral : 18.955 91.805 3624 Min Nonbonded Distance : 0.439 Molprobity Statistics. All-atom Clashscore : 210.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (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 TRP 0.020 0.004 TRP B 344 HIS 0.004 0.000 HIS K 354 PHE 0.033 0.002 PHE K 113 TYR 0.369 0.011 TYR A 399 ARG 0.086 0.002 ARG A 402 *********************** 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 : 1.259 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: B 122 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7780 (mttt) REVERT: B 210 ILE cc_start: 0.8044 (mt) cc_final: 0.7747 (mm) REVERT: B 293 MET cc_start: 0.6417 (mtp) cc_final: 0.6210 (mtp) REVERT: B 336 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7157 (mttt) REVERT: B 359 ARG cc_start: 0.6333 (mtt180) cc_final: 0.4900 (mtt180) REVERT: A 22 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: A 164 LYS cc_start: 0.4698 (OUTLIER) cc_final: 0.3022 (mmtp) REVERT: A 212 ILE cc_start: 0.8030 (mm) cc_final: 0.7747 (mm) REVERT: A 220 GLU cc_start: 0.3323 (OUTLIER) cc_final: 0.2577 (pp20) REVERT: A 266 HIS cc_start: 0.6925 (m90) cc_final: 0.6330 (m90) REVERT: A 303 VAL cc_start: 0.8192 (p) cc_final: 0.7169 (p) REVERT: A 396 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7716 (t0) outliers start: 165 outliers final: 67 residues processed: 337 average time/residue: 0.3032 time to fit residues: 129.8797 Evaluate side-chains 182 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 109 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 191 GLN 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 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 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 266 LEU 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 99 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 280 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.090500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.076038 restraints weight = 44191.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.078530 restraints weight = 24998.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.080201 restraints weight = 16072.398| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 9681 Z= 0.440 Angle : 1.072 16.593 13128 Z= 0.565 Chirality : 0.058 0.373 1461 Planarity : 0.010 0.102 1703 Dihedral : 15.521 87.334 1588 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 46.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 11.65 % Allowed : 21.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1191 helix: 0.04 (0.19), residues: 575 sheet: 1.17 (0.37), residues: 185 loop : -0.59 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B 21 HIS 0.013 0.003 HIS A 393 PHE 0.045 0.004 PHE B 260 TYR 0.143 0.005 TYR A 224 ARG 0.012 0.001 ARG K 181 *********************** 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 286 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 166 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.6187 (mm-30) REVERT: B 14 ASN cc_start: 0.7581 (m-40) cc_final: 0.7120 (m-40) REVERT: B 22 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6992 (pp20) REVERT: B 23 VAL cc_start: 0.8760 (p) cc_final: 0.8132 (m) REVERT: B 31 ASP cc_start: 0.3212 (OUTLIER) cc_final: 0.2894 (t0) REVERT: B 122 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.7841 (mtpt) REVERT: B 147 MET cc_start: 0.7275 (pmm) cc_final: 0.6837 (pmm) REVERT: B 155 ILE cc_start: 0.7547 (pt) cc_final: 0.7235 (tp) REVERT: B 158 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: B 216 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7853 (mmtt) REVERT: B 227 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7337 (t-170) REVERT: B 228 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8281 (tt) REVERT: B 280 GLN cc_start: 0.7286 (pt0) cc_final: 0.7015 (pt0) REVERT: B 291 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8280 (pp30) REVERT: B 293 MET cc_start: 0.7900 (mtp) cc_final: 0.7417 (ptt) REVERT: B 331 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8609 (mm) REVERT: B 336 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8139 (mttt) REVERT: A 18 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7437 (p0) REVERT: A 40 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6676 (mmtp) REVERT: A 52 PHE cc_start: 0.6307 (m-10) cc_final: 0.5816 (m-10) REVERT: A 86 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8667 (tp) REVERT: A 164 LYS cc_start: 0.5058 (OUTLIER) cc_final: 0.4595 (tppt) REVERT: A 204 VAL cc_start: 0.5890 (OUTLIER) cc_final: 0.5598 (p) REVERT: A 212 ILE cc_start: 0.8168 (mm) cc_final: 0.7825 (mm) REVERT: A 220 GLU cc_start: 0.4534 (OUTLIER) cc_final: 0.3260 (pp20) REVERT: A 242 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5573 (tm) REVERT: A 338 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8022 (tppp) REVERT: A 371 VAL cc_start: 0.3924 (OUTLIER) cc_final: 0.3681 (t) REVERT: K 68 PHE cc_start: 0.6605 (m-80) cc_final: 0.6028 (m-80) REVERT: K 101 ILE cc_start: 0.9292 (mt) cc_final: 0.9075 (tp) REVERT: K 177 ASP cc_start: 0.7870 (t70) cc_final: 0.7572 (t70) REVERT: K 215 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.6091 (pm20) REVERT: K 239 PHE cc_start: 0.8324 (t80) cc_final: 0.8121 (t80) REVERT: K 261 LEU cc_start: 0.9376 (tp) cc_final: 0.9142 (tp) REVERT: K 263 LEU cc_start: 0.8918 (mm) cc_final: 0.8367 (mt) outliers start: 120 outliers final: 48 residues processed: 256 average time/residue: 0.2827 time to fit residues: 93.8743 Evaluate side-chains 190 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 121 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 252 LYS 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 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 86 LEU 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 204 VAL Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 ARG 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 50 VAL Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 272 ILE 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 45 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 28 HIS ** 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 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.087948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.073162 restraints weight = 44770.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.075470 restraints weight = 25144.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.076978 restraints weight = 16320.387| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.7065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 9681 Z= 0.336 Angle : 0.901 16.440 13128 Z= 0.469 Chirality : 0.049 0.357 1461 Planarity : 0.008 0.082 1703 Dihedral : 13.414 87.651 1502 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 36.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 9.81 % Allowed : 23.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1191 helix: 0.12 (0.20), residues: 569 sheet: 0.69 (0.36), residues: 190 loop : -0.74 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP B 101 HIS 0.010 0.002 HIS B 105 PHE 0.028 0.003 PHE B 260 TYR 0.148 0.003 TYR A 224 ARG 0.009 0.001 ARG A 156 *********************** 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 245 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 144 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASN cc_start: 0.7168 (OUTLIER) cc_final: 0.6738 (m-40) REVERT: B 103 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8128 (mptt) REVERT: B 122 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8017 (mtmt) REVERT: B 145 SER cc_start: 0.7883 (OUTLIER) cc_final: 0.7642 (p) REVERT: B 155 ILE cc_start: 0.7940 (pt) cc_final: 0.7592 (mm) REVERT: B 156 ARG cc_start: 0.7854 (tpt90) cc_final: 0.6905 (tpp80) REVERT: B 227 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7619 (t-170) REVERT: B 280 GLN cc_start: 0.7341 (pt0) cc_final: 0.7066 (pt0) REVERT: B 300 MET cc_start: 0.8164 (tpp) cc_final: 0.7581 (mmt) REVERT: B 329 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8568 (tm-30) REVERT: B 336 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8033 (mttt) REVERT: B 379 LYS cc_start: 0.8536 (pttp) cc_final: 0.8124 (pttp) REVERT: A 52 PHE cc_start: 0.6122 (m-10) cc_final: 0.5718 (m-10) REVERT: A 204 VAL cc_start: 0.6278 (OUTLIER) cc_final: 0.6061 (p) REVERT: A 205 ASP cc_start: 0.6687 (OUTLIER) cc_final: 0.6157 (m-30) REVERT: A 209 ILE cc_start: 0.7475 (mt) cc_final: 0.6850 (mt) REVERT: A 212 ILE cc_start: 0.8254 (mm) cc_final: 0.7943 (mm) REVERT: A 242 LEU cc_start: 0.5658 (OUTLIER) cc_final: 0.5229 (tm) REVERT: A 267 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.5903 (p90) REVERT: A 432 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6031 (t80) REVERT: K 177 ASP cc_start: 0.7961 (t70) cc_final: 0.7687 (t70) REVERT: K 304 GLU cc_start: 0.7992 (tp30) cc_final: 0.7765 (tm-30) REVERT: K 367 GLN cc_start: 0.6694 (OUTLIER) cc_final: 0.6023 (tp-100) outliers start: 101 outliers final: 51 residues processed: 218 average time/residue: 0.2644 time to fit residues: 75.9163 Evaluate side-chains 181 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 118 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 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 145 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 227 HIS 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 334 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 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 308 ARG 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 33 ARG Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 266 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN B 134 GLN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN A 186 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS K 244 HIS ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.085027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.070287 restraints weight = 44330.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.072442 restraints weight = 24677.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.073832 restraints weight = 16052.285| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.8026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9681 Z= 0.320 Angle : 0.840 16.294 13128 Z= 0.439 Chirality : 0.049 0.467 1461 Planarity : 0.007 0.087 1703 Dihedral : 12.410 89.182 1457 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 33.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 7.67 % Allowed : 25.83 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.23), residues: 1191 helix: 0.15 (0.20), residues: 581 sheet: 0.52 (0.37), residues: 200 loop : -0.84 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 21 HIS 0.009 0.002 HIS B 190 PHE 0.024 0.002 PHE B 385 TYR 0.142 0.003 TYR A 224 ARG 0.006 0.001 ARG A 221 *********************** 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 201 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 122 time to evaluate : 1.052 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: 0.8312 (OUTLIER) cc_final: 0.7622 (mttt) REVERT: B 114 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8251 (t0) REVERT: B 122 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8045 (mtmt) REVERT: B 156 ARG cc_start: 0.7967 (tpt90) cc_final: 0.7210 (tpp80) REVERT: B 336 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7890 (mttt) REVERT: B 378 PHE cc_start: 0.8371 (m-10) cc_final: 0.8165 (m-10) REVERT: A 52 PHE cc_start: 0.6263 (m-10) cc_final: 0.5762 (m-10) REVERT: A 204 VAL cc_start: 0.6648 (OUTLIER) cc_final: 0.6406 (m) REVERT: A 209 ILE cc_start: 0.7553 (mt) cc_final: 0.7212 (mt) REVERT: A 212 ILE cc_start: 0.8326 (mm) cc_final: 0.7993 (mm) REVERT: A 267 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.5793 (p90) REVERT: A 313 MET cc_start: 0.6007 (mtp) cc_final: 0.5173 (mtt) REVERT: A 425 MET cc_start: 0.9220 (mmm) cc_final: 0.8926 (mmm) REVERT: A 432 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.5955 (t80) REVERT: K 115 MET cc_start: 0.7592 (tpt) cc_final: 0.7302 (ptt) REVERT: K 177 ASP cc_start: 0.7992 (t70) cc_final: 0.7689 (t70) REVERT: K 239 PHE cc_start: 0.8601 (t80) cc_final: 0.8220 (t80) REVERT: K 245 MET cc_start: 0.8374 (mtm) cc_final: 0.7919 (mpp) REVERT: K 367 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.5835 (tm-30) outliers start: 79 outliers final: 44 residues processed: 183 average time/residue: 0.2651 time to fit residues: 64.9160 Evaluate side-chains 163 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 111 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 276 ARG 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 376 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 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 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 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 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 33 ARG 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 266 LEU 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 52 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 11 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 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 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.084416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.069727 restraints weight = 44898.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.071851 restraints weight = 25137.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.073229 restraints weight = 16410.146| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.8558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9681 Z= 0.284 Angle : 0.816 16.146 13128 Z= 0.420 Chirality : 0.047 0.478 1461 Planarity : 0.007 0.096 1703 Dihedral : 12.074 94.888 1449 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 30.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 7.18 % Allowed : 25.83 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1191 helix: 0.17 (0.20), residues: 576 sheet: 0.53 (0.37), residues: 191 loop : -0.81 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 21 HIS 0.015 0.002 HIS B 28 PHE 0.029 0.002 PHE B 294 TYR 0.141 0.003 TYR A 224 ARG 0.006 0.001 ARG A 215 *********************** 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 197 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 123 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7698 (mttt) REVERT: B 122 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8046 (mtmt) REVERT: B 216 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7313 (mtmm) REVERT: B 378 PHE cc_start: 0.8243 (m-10) cc_final: 0.8037 (m-10) REVERT: B 379 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8184 (pttp) REVERT: A 40 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6577 (mmmm) REVERT: A 52 PHE cc_start: 0.6432 (m-10) cc_final: 0.5960 (m-10) REVERT: A 204 VAL cc_start: 0.7033 (OUTLIER) cc_final: 0.6776 (m) REVERT: A 209 ILE cc_start: 0.7715 (mt) cc_final: 0.7461 (mt) REVERT: A 212 ILE cc_start: 0.8377 (mm) cc_final: 0.8073 (mm) REVERT: A 220 GLU cc_start: 0.5954 (OUTLIER) cc_final: 0.5665 (pp20) REVERT: A 242 LEU cc_start: 0.5480 (OUTLIER) cc_final: 0.5218 (tm) REVERT: A 267 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.5661 (p90) REVERT: A 311 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6778 (mppt) REVERT: A 313 MET cc_start: 0.5932 (mtp) cc_final: 0.5085 (mtt) REVERT: A 373 ARG cc_start: 0.7254 (mpt180) cc_final: 0.6667 (mtt180) REVERT: A 425 MET cc_start: 0.9033 (mmm) cc_final: 0.8754 (mmm) REVERT: A 432 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.5973 (t80) REVERT: K 115 MET cc_start: 0.7588 (tpt) cc_final: 0.7367 (ptt) REVERT: K 177 ASP cc_start: 0.8120 (t70) cc_final: 0.7823 (t70) REVERT: K 245 MET cc_start: 0.8264 (mtm) cc_final: 0.7801 (mpp) REVERT: K 367 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.6293 (tm-30) outliers start: 74 outliers final: 47 residues processed: 180 average time/residue: 0.2677 time to fit residues: 63.6256 Evaluate side-chains 171 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 112 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 151 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 300 MET 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 334 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 379 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 204 VAL Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 308 ARG 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 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 33 ARG 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 261 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 367 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 104 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 89 optimal weight: 0.0770 chunk 60 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.084971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.070163 restraints weight = 44714.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.072277 restraints weight = 25274.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.073672 restraints weight = 16633.387| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.8955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9681 Z= 0.246 Angle : 0.811 19.387 13128 Z= 0.405 Chirality : 0.046 0.426 1461 Planarity : 0.007 0.089 1703 Dihedral : 12.072 93.404 1441 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 27.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 6.89 % Allowed : 25.92 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1191 helix: 0.26 (0.20), residues: 575 sheet: 0.57 (0.36), residues: 196 loop : -0.82 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 21 HIS 0.011 0.002 HIS B 28 PHE 0.027 0.002 PHE B 260 TYR 0.166 0.003 TYR A 224 ARG 0.005 0.001 ARG K 33 *********************** 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 189 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 118 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7658 (mttt) REVERT: B 122 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8103 (mtmt) REVERT: B 147 MET cc_start: 0.7170 (pmm) cc_final: 0.6905 (pmm) REVERT: B 216 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7163 (mtmm) REVERT: B 233 MET cc_start: 0.6562 (mmt) cc_final: 0.6348 (mmt) REVERT: B 257 MET cc_start: 0.8985 (tpp) cc_final: 0.8513 (mmt) REVERT: B 379 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8478 (pttp) REVERT: A 132 LEU cc_start: 0.7201 (mp) cc_final: 0.6820 (mp) REVERT: A 204 VAL cc_start: 0.7432 (OUTLIER) cc_final: 0.7182 (m) REVERT: A 212 ILE cc_start: 0.8275 (mm) cc_final: 0.7960 (mm) REVERT: A 220 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5661 (pp20) REVERT: A 242 LEU cc_start: 0.5399 (OUTLIER) cc_final: 0.5177 (tm) REVERT: A 267 PHE cc_start: 0.6626 (OUTLIER) cc_final: 0.5632 (p90) REVERT: A 302 MET cc_start: 0.8158 (tpt) cc_final: 0.7806 (tpt) REVERT: A 313 MET cc_start: 0.5954 (mtp) cc_final: 0.5103 (mtt) REVERT: A 373 ARG cc_start: 0.7201 (mpt180) cc_final: 0.6912 (mtt180) REVERT: A 425 MET cc_start: 0.9112 (mmm) cc_final: 0.8811 (mmm) REVERT: A 432 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.5936 (t80) REVERT: K 115 MET cc_start: 0.7720 (tpt) cc_final: 0.7421 (ptt) REVERT: K 177 ASP cc_start: 0.8024 (t70) cc_final: 0.7729 (t70) REVERT: K 245 MET cc_start: 0.8385 (mtm) cc_final: 0.7955 (mpp) outliers start: 71 outliers final: 47 residues processed: 174 average time/residue: 0.2701 time to fit residues: 62.1048 Evaluate side-chains 162 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 106 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 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 151 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 125 LEU 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 204 VAL 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 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 33 ARG 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 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 47 optimal weight: 0.0870 chunk 40 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.084506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.069654 restraints weight = 45047.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.071774 restraints weight = 25469.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.073146 restraints weight = 16723.058| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.9323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9681 Z= 0.262 Angle : 0.792 18.040 13128 Z= 0.402 Chirality : 0.046 0.370 1461 Planarity : 0.007 0.091 1703 Dihedral : 11.896 96.002 1435 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 27.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 6.99 % Allowed : 25.92 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1191 helix: 0.33 (0.20), residues: 575 sheet: 0.63 (0.37), residues: 185 loop : -0.94 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 21 HIS 0.016 0.002 HIS B 28 PHE 0.031 0.002 PHE B 260 TYR 0.196 0.003 TYR A 224 ARG 0.008 0.001 ARG K 83 *********************** 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 191 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 119 time to evaluate : 1.194 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: B 103 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7736 (mttt) REVERT: B 122 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8140 (mtmt) REVERT: B 216 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7046 (mtmm) REVERT: B 306 ARG cc_start: 0.7859 (tpp-160) cc_final: 0.7636 (tpp-160) REVERT: B 379 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8214 (tppt) REVERT: A 40 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6463 (mmtp) REVERT: A 52 PHE cc_start: 0.6273 (m-10) cc_final: 0.5787 (m-80) REVERT: A 132 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6324 (mt) REVERT: A 203 MET cc_start: 0.6860 (mpp) cc_final: 0.6449 (mpp) REVERT: A 204 VAL cc_start: 0.7875 (p) cc_final: 0.7585 (p) REVERT: A 212 ILE cc_start: 0.8247 (mm) cc_final: 0.7938 (mm) REVERT: A 220 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5644 (pp20) REVERT: A 267 PHE cc_start: 0.6590 (OUTLIER) cc_final: 0.5518 (p90) REVERT: A 313 MET cc_start: 0.6121 (mtp) cc_final: 0.5301 (mtt) REVERT: A 373 ARG cc_start: 0.7378 (mpt180) cc_final: 0.7103 (mtt180) REVERT: A 425 MET cc_start: 0.9104 (mmm) cc_final: 0.8821 (mmm) REVERT: A 432 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.5951 (t80) REVERT: K 115 MET cc_start: 0.7649 (tpt) cc_final: 0.7378 (ptt) REVERT: K 177 ASP cc_start: 0.8012 (t70) cc_final: 0.7701 (t70) outliers start: 72 outliers final: 54 residues processed: 174 average time/residue: 0.2811 time to fit residues: 64.8741 Evaluate side-chains 170 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 107 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 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 151 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 300 MET 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 376 GLU Chi-restraints excluded: chain B residue 379 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 93 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 LEU 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 217 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 33 ARG Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS B 8 GLN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 173 ASN ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.082565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.067798 restraints weight = 45457.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.069848 restraints weight = 25665.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.071196 restraints weight = 16864.824| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.9707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 9681 Z= 0.310 Angle : 0.823 17.764 13128 Z= 0.423 Chirality : 0.046 0.186 1461 Planarity : 0.007 0.093 1703 Dihedral : 11.741 97.808 1435 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 28.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.89 % Rotamer: Outliers : 7.28 % Allowed : 27.09 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1191 helix: 0.30 (0.20), residues: 579 sheet: 0.39 (0.38), residues: 181 loop : -0.97 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 21 HIS 0.020 0.002 HIS B 28 PHE 0.047 0.003 PHE B 378 TYR 0.175 0.003 TYR A 224 ARG 0.007 0.001 ARG A 105 *********************** 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 194 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 119 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7669 (mttt) REVERT: B 122 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8260 (mtmt) REVERT: B 216 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6905 (mtmm) REVERT: B 252 LYS cc_start: 0.5415 (OUTLIER) cc_final: 0.5062 (ptpt) REVERT: B 257 MET cc_start: 0.9178 (tpp) cc_final: 0.8454 (mmt) REVERT: B 299 MET cc_start: 0.7602 (tpp) cc_final: 0.7319 (tpt) REVERT: B 306 ARG cc_start: 0.7905 (tpp-160) cc_final: 0.7702 (tpp-160) REVERT: A 40 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6232 (mmtp) REVERT: A 52 PHE cc_start: 0.6386 (m-10) cc_final: 0.5980 (m-80) REVERT: A 132 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.6786 (mt) REVERT: A 203 MET cc_start: 0.7034 (mpp) cc_final: 0.6709 (mpp) REVERT: A 212 ILE cc_start: 0.8254 (mm) cc_final: 0.7961 (mm) REVERT: A 220 GLU cc_start: 0.6045 (OUTLIER) cc_final: 0.5552 (pp20) REVERT: A 267 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.5569 (p90) REVERT: A 313 MET cc_start: 0.6276 (mtp) cc_final: 0.5436 (mtt) REVERT: A 373 ARG cc_start: 0.7437 (mpt180) cc_final: 0.7189 (mtt180) REVERT: A 432 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.5990 (t80) REVERT: K 115 MET cc_start: 0.7612 (tpt) cc_final: 0.7379 (ptt) REVERT: K 177 ASP cc_start: 0.8017 (t70) cc_final: 0.7714 (t70) REVERT: K 228 MET cc_start: 0.8535 (mmt) cc_final: 0.8299 (mmt) REVERT: K 245 MET cc_start: 0.8527 (mtm) cc_final: 0.8133 (mpp) REVERT: K 263 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8507 (pp) outliers start: 75 outliers final: 51 residues processed: 177 average time/residue: 0.2781 time to fit residues: 64.8309 Evaluate side-chains 170 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 109 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 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 170 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 132 LEU 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 217 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 THR 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 353 VAL Chi-restraints excluded: chain A residue 361 THR 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 33 ARG 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 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 89 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** 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 = 0.4132 r_free = 0.4132 target = 0.081987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.067191 restraints weight = 45374.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.069248 restraints weight = 25789.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.070611 restraints weight = 17000.970| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 1.0138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9681 Z= 0.304 Angle : 0.854 17.137 13128 Z= 0.434 Chirality : 0.047 0.227 1461 Planarity : 0.007 0.096 1703 Dihedral : 11.761 96.704 1435 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 27.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 6.60 % Allowed : 27.48 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.23), residues: 1191 helix: 0.25 (0.20), residues: 581 sheet: 0.38 (0.39), residues: 179 loop : -0.93 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 21 HIS 0.015 0.003 HIS B 28 PHE 0.041 0.003 PHE B 260 TYR 0.167 0.003 TYR A 224 ARG 0.008 0.001 ARG A 105 *********************** 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 182 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 114 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7604 (mttt) REVERT: B 122 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8278 (mtmt) REVERT: B 216 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6943 (mtmm) REVERT: B 252 LYS cc_start: 0.5767 (OUTLIER) cc_final: 0.5251 (ptpt) REVERT: A 40 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6682 (mmtp) REVERT: A 52 PHE cc_start: 0.6359 (m-10) cc_final: 0.5892 (m-80) REVERT: A 132 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.6940 (mt) REVERT: A 149 PHE cc_start: 0.7783 (t80) cc_final: 0.7384 (m-80) REVERT: A 212 ILE cc_start: 0.8307 (mm) cc_final: 0.8015 (mm) REVERT: A 220 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5596 (pp20) REVERT: A 267 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.5815 (p90) REVERT: A 313 MET cc_start: 0.6349 (mtp) cc_final: 0.5540 (mtt) REVERT: A 373 ARG cc_start: 0.7577 (mpt180) cc_final: 0.7282 (mtt180) REVERT: A 432 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.6054 (t80) REVERT: K 70 MET cc_start: 0.7725 (tpt) cc_final: 0.7316 (tpp) REVERT: K 163 ILE cc_start: 0.6386 (mt) cc_final: 0.6170 (mt) REVERT: K 177 ASP cc_start: 0.7983 (t70) cc_final: 0.7674 (t70) REVERT: K 215 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.4887 (pm20) REVERT: K 228 MET cc_start: 0.8631 (mmt) cc_final: 0.8365 (mmt) REVERT: K 245 MET cc_start: 0.8511 (mtm) cc_final: 0.8101 (mpp) outliers start: 68 outliers final: 50 residues processed: 169 average time/residue: 0.2759 time to fit residues: 62.0065 Evaluate side-chains 164 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 104 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 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 170 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 132 LEU 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 217 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 361 THR 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 33 ARG 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 261 LEU Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 0.0470 chunk 108 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.082757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.067709 restraints weight = 45604.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.069773 restraints weight = 25851.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.071142 restraints weight = 17080.007| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 1.0428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 9681 Z= 0.282 Angle : 0.855 16.884 13128 Z= 0.433 Chirality : 0.047 0.277 1461 Planarity : 0.010 0.306 1703 Dihedral : 11.367 86.417 1432 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 27.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.27 % Favored : 96.64 % Rotamer: Outliers : 5.92 % Allowed : 28.25 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.23), residues: 1191 helix: 0.29 (0.21), residues: 569 sheet: 0.42 (0.39), residues: 179 loop : -0.88 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 21 HIS 0.013 0.002 HIS K 354 PHE 0.035 0.002 PHE B 260 TYR 0.162 0.003 TYR A 224 ARG 0.032 0.001 ARG B 251 ********************** 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 180 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 119 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7569 (mttt) REVERT: B 122 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8263 (mtmt) REVERT: B 216 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6713 (mtmm) REVERT: B 249 ASP cc_start: 0.7425 (t70) cc_final: 0.6265 (t0) REVERT: B 257 MET cc_start: 0.9057 (tpp) cc_final: 0.8806 (tpt) REVERT: B 306 ARG cc_start: 0.7894 (tpp-160) cc_final: 0.7642 (tpp-160) REVERT: A 40 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6447 (mmtp) REVERT: A 52 PHE cc_start: 0.6304 (m-10) cc_final: 0.5833 (m-80) REVERT: A 132 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7133 (mt) REVERT: A 149 PHE cc_start: 0.7640 (t80) cc_final: 0.7299 (m-80) REVERT: A 154 MET cc_start: 0.8647 (mmp) cc_final: 0.8344 (mmt) REVERT: A 203 MET cc_start: 0.7175 (mpp) cc_final: 0.6668 (mpp) REVERT: A 212 ILE cc_start: 0.8279 (mm) cc_final: 0.7989 (mm) REVERT: A 220 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.5627 (pp20) REVERT: A 267 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.5652 (p90) REVERT: A 313 MET cc_start: 0.6414 (mtp) cc_final: 0.5549 (mtt) REVERT: A 432 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.6108 (t80) REVERT: K 70 MET cc_start: 0.7684 (tpt) cc_final: 0.7285 (tpp) REVERT: K 163 ILE cc_start: 0.6387 (mt) cc_final: 0.6166 (mt) REVERT: K 177 ASP cc_start: 0.7929 (t70) cc_final: 0.7619 (t70) REVERT: K 215 GLU cc_start: 0.5265 (OUTLIER) cc_final: 0.4927 (pm20) REVERT: K 228 MET cc_start: 0.8712 (mmt) cc_final: 0.8457 (mmt) REVERT: K 239 PHE cc_start: 0.8747 (t80) cc_final: 0.8389 (t80) REVERT: K 245 MET cc_start: 0.8486 (mtm) cc_final: 0.8046 (mpp) REVERT: K 302 LEU cc_start: 0.8561 (tp) cc_final: 0.8311 (pp) outliers start: 61 outliers final: 49 residues processed: 167 average time/residue: 0.2777 time to fit residues: 60.5317 Evaluate side-chains 164 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 106 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET 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 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 132 LEU 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 255 PHE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 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 33 ARG Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.082497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.067649 restraints weight = 45321.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.069715 restraints weight = 25855.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.071028 restraints weight = 17034.577| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 1.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 9681 Z= 0.312 Angle : 0.936 35.176 13128 Z= 0.474 Chirality : 0.048 0.349 1461 Planarity : 0.007 0.094 1703 Dihedral : 12.317 179.186 1432 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 26.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.95 % Favored : 95.89 % Rotamer: Outliers : 5.92 % Allowed : 28.64 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.23), residues: 1191 helix: 0.30 (0.21), residues: 569 sheet: 0.42 (0.39), residues: 180 loop : -0.99 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 21 HIS 0.013 0.002 HIS K 354 PHE 0.067 0.003 PHE B 260 TYR 0.158 0.003 TYR A 224 ARG 0.036 0.001 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4473.53 seconds wall clock time: 79 minutes 3.46 seconds (4743.46 seconds total)