Starting phenix.real_space_refine on Fri Feb 14 03:33:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ta3_10421/02_2025/6ta3_10421.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ta3_10421/02_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_10421/02_2025/6ta3_10421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ta3_10421/02_2025/6ta3_10421.map" model { file = "/net/cci-nas-00/data/ceres_data/6ta3_10421/02_2025/6ta3_10421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ta3_10421/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.44, per 1000 atoms: 0.78 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: 3.53 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: 0.94 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: 3.04 Time building geometry restraints manager: 3.81 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: 0.010 Normalize map: mean=0, sd=1: 7.210 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.840 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.270 ------------------------------------------------------------------------------- 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 : 1.122 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: 0.3116 time to fit residues: 133.2865 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 : 1.100 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.076038 restraints weight = 44191.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.078537 restraints weight = 24998.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.080205 restraints weight = 16059.049| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 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 : 1.121 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: 0.6407 (OUTLIER) cc_final: 0.6194 (mm-30) REVERT: B 14 ASN cc_start: 0.7581 (m-40) cc_final: 0.7120 (m-40) REVERT: B 22 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6993 (pp20) REVERT: B 23 VAL cc_start: 0.8760 (p) cc_final: 0.8131 (m) REVERT: B 31 ASP cc_start: 0.3214 (OUTLIER) cc_final: 0.2897 (t0) REVERT: B 122 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.7841 (mtpt) REVERT: B 147 MET cc_start: 0.7277 (pmm) cc_final: 0.6837 (pmm) REVERT: B 155 ILE cc_start: 0.7546 (pt) cc_final: 0.7235 (tp) REVERT: B 158 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6281 (mp0) REVERT: B 216 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7855 (mmtt) REVERT: B 227 HIS cc_start: 0.7574 (OUTLIER) cc_final: 0.7337 (t-170) REVERT: B 228 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8280 (tt) REVERT: B 280 GLN cc_start: 0.7287 (pt0) cc_final: 0.7015 (pt0) REVERT: B 291 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8283 (pp30) REVERT: B 293 MET cc_start: 0.7903 (mtp) cc_final: 0.7418 (ptt) REVERT: B 331 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8609 (mm) REVERT: B 336 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8137 (mttt) REVERT: A 18 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7436 (p0) REVERT: A 40 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6684 (mmtp) REVERT: A 52 PHE cc_start: 0.6309 (m-10) cc_final: 0.5819 (m-10) REVERT: A 86 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8666 (tp) REVERT: A 164 LYS cc_start: 0.5047 (OUTLIER) cc_final: 0.4591 (tppt) REVERT: A 204 VAL cc_start: 0.5889 (OUTLIER) cc_final: 0.5594 (p) REVERT: A 212 ILE cc_start: 0.8176 (mm) cc_final: 0.7831 (mm) REVERT: A 220 GLU cc_start: 0.4514 (OUTLIER) cc_final: 0.3244 (pp20) REVERT: A 242 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5577 (tm) REVERT: A 338 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8018 (tppp) REVERT: A 371 VAL cc_start: 0.3928 (OUTLIER) cc_final: 0.3681 (t) REVERT: K 68 PHE cc_start: 0.6613 (m-80) cc_final: 0.6029 (m-80) REVERT: K 101 ILE cc_start: 0.9275 (mt) cc_final: 0.9049 (tp) REVERT: K 177 ASP cc_start: 0.7858 (t70) cc_final: 0.7551 (t70) REVERT: K 215 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.6083 (pm20) REVERT: K 261 LEU cc_start: 0.9366 (tp) cc_final: 0.9116 (tp) REVERT: K 263 LEU cc_start: 0.8901 (mm) cc_final: 0.8345 (mt) outliers start: 120 outliers final: 48 residues processed: 256 average time/residue: 0.2802 time to fit residues: 93.3535 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 : 1.082 ------------------------------------------------------------------------------- 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: 0.9980 chunk 100 optimal weight: 0.0040 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 5 optimal weight: 0.0670 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 overall best weight: 0.3128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.090448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.075558 restraints weight = 44504.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.077990 restraints weight = 25154.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.079574 restraints weight = 16325.079| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.6964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 9681 Z= 0.306 Angle : 0.899 16.434 13128 Z= 0.462 Chirality : 0.049 0.348 1461 Planarity : 0.008 0.080 1703 Dihedral : 13.397 90.671 1502 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 34.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 9.51 % Allowed : 23.59 % 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: -0.21 (0.22), residues: 1191 helix: 0.07 (0.19), residues: 573 sheet: 0.82 (0.35), residues: 197 loop : -0.73 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP B 21 HIS 0.010 0.002 HIS B 105 PHE 0.031 0.003 PHE B 260 TYR 0.147 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 247 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 149 time to evaluate : 1.025 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 3 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5906 (mm-30) REVERT: B 14 ASN cc_start: 0.6949 (OUTLIER) cc_final: 0.6593 (m-40) REVERT: B 103 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8139 (mptt) REVERT: B 114 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8337 (t0) REVERT: B 122 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.7915 (mtmt) REVERT: B 155 ILE cc_start: 0.7839 (pt) cc_final: 0.7637 (mm) REVERT: B 276 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6044 (tmm160) REVERT: B 280 GLN cc_start: 0.7238 (pt0) cc_final: 0.6714 (pt0) REVERT: B 300 MET cc_start: 0.8163 (tpp) cc_final: 0.7642 (mmt) REVERT: B 329 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8504 (tm-30) REVERT: B 336 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8090 (mttt) REVERT: B 376 GLU cc_start: 0.4965 (OUTLIER) cc_final: 0.4600 (mp0) REVERT: B 379 LYS cc_start: 0.8583 (pttp) cc_final: 0.8323 (pttp) REVERT: A 18 ASN cc_start: 0.7576 (OUTLIER) cc_final: 0.7301 (p0) REVERT: A 52 PHE cc_start: 0.6141 (m-10) cc_final: 0.5871 (m-10) REVERT: A 203 MET cc_start: 0.5322 (mpp) cc_final: 0.5076 (mpp) REVERT: A 205 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6329 (m-30) REVERT: A 209 ILE cc_start: 0.7419 (mt) cc_final: 0.6807 (mt) REVERT: A 212 ILE cc_start: 0.8221 (mm) cc_final: 0.7918 (mm) REVERT: A 242 LEU cc_start: 0.5498 (OUTLIER) cc_final: 0.5080 (tm) REVERT: A 267 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.5381 (p90) REVERT: A 311 LYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6663 (mppt) REVERT: A 432 TYR cc_start: 0.7168 (OUTLIER) cc_final: 0.6000 (t80) REVERT: K 177 ASP cc_start: 0.7924 (t70) cc_final: 0.7631 (t70) REVERT: K 215 GLU cc_start: 0.5762 (OUTLIER) cc_final: 0.5349 (pm20) REVERT: K 239 PHE cc_start: 0.8338 (t80) cc_final: 0.8118 (t80) REVERT: K 367 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.6018 (tp-100) outliers start: 98 outliers final: 42 residues processed: 222 average time/residue: 0.2611 time to fit residues: 77.1009 Evaluate side-chains 182 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 124 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 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 375 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR 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 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 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: 0.0870 chunk 26 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 78 optimal weight: 0.0060 chunk 84 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 59 optimal weight: 0.0020 chunk 70 optimal weight: 2.9990 overall best weight: 0.2782 ------------------------------------------------------------------------------- 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 52 ASN B 134 GLN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** 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 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.089637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.074945 restraints weight = 43810.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.077257 restraints weight = 24503.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.078767 restraints weight = 15824.861| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.7804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9681 Z= 0.265 Angle : 0.837 16.517 13128 Z= 0.426 Chirality : 0.046 0.188 1461 Planarity : 0.007 0.082 1703 Dihedral : 12.137 88.617 1453 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 7.57 % Allowed : 24.17 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.22), residues: 1191 helix: 0.04 (0.19), residues: 575 sheet: 0.72 (0.36), residues: 199 loop : -0.89 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 21 HIS 0.010 0.002 HIS B 227 PHE 0.027 0.002 PHE K 28 TYR 0.140 0.003 TYR A 224 ARG 0.008 0.001 ARG A 64 *********************** 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 218 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 140 time to evaluate : 1.090 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: 0.8203 (OUTLIER) cc_final: 0.7590 (mttt) REVERT: B 122 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7907 (mtmt) REVERT: B 280 GLN cc_start: 0.7234 (pt0) cc_final: 0.6554 (pp30) REVERT: B 300 MET cc_start: 0.8357 (tpp) cc_final: 0.7627 (mmt) REVERT: B 336 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7958 (mttt) REVERT: B 379 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8288 (pttp) REVERT: A 52 PHE cc_start: 0.6087 (m-10) cc_final: 0.5479 (m-10) REVERT: A 154 MET cc_start: 0.7165 (tpp) cc_final: 0.6867 (mmp) REVERT: A 182 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8063 (p) REVERT: A 209 ILE cc_start: 0.7440 (mt) cc_final: 0.7097 (mt) REVERT: A 212 ILE cc_start: 0.8291 (mm) cc_final: 0.7982 (mm) REVERT: A 220 GLU cc_start: 0.5527 (OUTLIER) cc_final: 0.5076 (pp20) REVERT: A 242 LEU cc_start: 0.5407 (OUTLIER) cc_final: 0.5129 (tm) REVERT: A 267 PHE cc_start: 0.6717 (OUTLIER) cc_final: 0.5551 (p90) REVERT: A 425 MET cc_start: 0.8974 (mmm) cc_final: 0.8686 (mmm) REVERT: A 432 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.5880 (t80) REVERT: K 115 MET cc_start: 0.7555 (tpt) cc_final: 0.7200 (ptt) REVERT: K 177 ASP cc_start: 0.8009 (t70) cc_final: 0.7699 (t70) REVERT: K 181 ARG cc_start: 0.6468 (OUTLIER) cc_final: 0.5491 (tpm170) REVERT: K 239 PHE cc_start: 0.8369 (t80) cc_final: 0.8128 (t80) REVERT: K 261 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9207 (tp) outliers start: 78 outliers final: 40 residues processed: 192 average time/residue: 0.2584 time to fit residues: 66.2085 Evaluate side-chains 170 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 119 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 320 ARG 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 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 136 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 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 351 PHE 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 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 272 ILE Chi-restraints excluded: chain K residue 315 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 0.0870 chunk 91 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 111 optimal weight: 0.0770 chunk 117 optimal weight: 0.0870 chunk 3 optimal weight: 2.9990 overall best weight: 0.2894 ------------------------------------------------------------------------------- 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 ** 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 101 ASN ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.089169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.074209 restraints weight = 43879.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.076554 restraints weight = 24376.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.078106 restraints weight = 15796.574| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.8322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9681 Z= 0.266 Angle : 0.856 18.747 13128 Z= 0.426 Chirality : 0.046 0.182 1461 Planarity : 0.007 0.108 1703 Dihedral : 12.038 88.509 1441 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 30.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 7.09 % Allowed : 25.24 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.38 (0.23), residues: 1191 helix: -0.09 (0.19), residues: 585 sheet: 0.90 (0.37), residues: 189 loop : -0.85 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 21 HIS 0.009 0.001 HIS A 192 PHE 0.031 0.002 PHE B 294 TYR 0.138 0.003 TYR A 224 ARG 0.006 0.001 ARG B 241 *********************** 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 205 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 132 time to evaluate : 1.073 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 122 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7939 (mtmt) REVERT: B 156 ARG cc_start: 0.8064 (tpt90) cc_final: 0.6795 (tmm-80) REVERT: B 252 LYS cc_start: 0.6336 (OUTLIER) cc_final: 0.5540 (ptpt) REVERT: B 299 MET cc_start: 0.7653 (mmt) cc_final: 0.7396 (tpt) REVERT: B 329 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8362 (tm-30) REVERT: B 336 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8012 (mttp) REVERT: B 379 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8195 (pttp) REVERT: A 52 PHE cc_start: 0.6028 (m-10) cc_final: 0.5572 (m-10) REVERT: A 150 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8108 (m) REVERT: A 154 MET cc_start: 0.7074 (tpp) cc_final: 0.6684 (mmp) REVERT: A 182 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7947 (p) REVERT: A 212 ILE cc_start: 0.8251 (mm) cc_final: 0.7925 (mm) REVERT: A 220 GLU cc_start: 0.5751 (OUTLIER) cc_final: 0.5344 (pp20) REVERT: A 242 LEU cc_start: 0.5322 (OUTLIER) cc_final: 0.5070 (tm) REVERT: A 267 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.5616 (p90) REVERT: A 313 MET cc_start: 0.5382 (mtp) cc_final: 0.4569 (mtt) REVERT: A 317 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7912 (mp) REVERT: A 425 MET cc_start: 0.8854 (mmm) cc_final: 0.8018 (mmm) REVERT: A 432 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.5885 (t80) REVERT: K 115 MET cc_start: 0.7540 (tpt) cc_final: 0.7308 (ptt) REVERT: K 177 ASP cc_start: 0.8026 (t70) cc_final: 0.7709 (t70) REVERT: K 239 PHE cc_start: 0.8529 (t80) cc_final: 0.7737 (t80) REVERT: K 245 MET cc_start: 0.8363 (mtm) cc_final: 0.7926 (mpp) outliers start: 73 outliers final: 48 residues processed: 178 average time/residue: 0.2575 time to fit residues: 61.2150 Evaluate side-chains 182 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 123 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 TYR 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 125 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 182 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 255 PHE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 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 266 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 104 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 60 optimal weight: 0.0970 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.3536 ------------------------------------------------------------------------------- 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 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.088452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.073382 restraints weight = 44062.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.075712 restraints weight = 24745.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.077274 restraints weight = 16132.631| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.8711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9681 Z= 0.259 Angle : 0.799 16.455 13128 Z= 0.403 Chirality : 0.045 0.186 1461 Planarity : 0.007 0.112 1703 Dihedral : 12.094 92.315 1437 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 7.18 % Allowed : 25.73 % 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: -0.36 (0.23), residues: 1191 helix: -0.01 (0.19), residues: 580 sheet: 0.78 (0.37), residues: 184 loop : -0.86 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 407 HIS 0.018 0.002 HIS B 28 PHE 0.024 0.002 PHE B 260 TYR 0.137 0.003 TYR A 224 ARG 0.010 0.001 ARG A 105 *********************** 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 210 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 136 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7600 (mttt) REVERT: B 122 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.7985 (mtmt) REVERT: B 156 ARG cc_start: 0.8178 (tpt90) cc_final: 0.7003 (tmm-80) REVERT: B 233 MET cc_start: 0.6884 (tpp) cc_final: 0.6174 (ptp) REVERT: A 103 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.7234 (t80) REVERT: A 150 THR cc_start: 0.8487 (m) cc_final: 0.8139 (m) REVERT: A 182 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.7906 (p) REVERT: A 212 ILE cc_start: 0.8217 (mm) cc_final: 0.7909 (mm) REVERT: A 220 GLU cc_start: 0.5866 (OUTLIER) cc_final: 0.5542 (pp20) REVERT: A 267 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.5750 (p90) REVERT: A 313 MET cc_start: 0.5454 (mtp) cc_final: 0.4639 (mtt) REVERT: A 317 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8002 (mp) REVERT: A 318 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8283 (mm) REVERT: A 425 MET cc_start: 0.8863 (mmm) cc_final: 0.8594 (mmm) REVERT: A 432 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6006 (t80) REVERT: K 28 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7323 (t80) REVERT: K 70 MET cc_start: 0.7825 (tpp) cc_final: 0.7406 (tpp) REVERT: K 115 MET cc_start: 0.7653 (tpt) cc_final: 0.7346 (ptt) REVERT: K 177 ASP cc_start: 0.7972 (t70) cc_final: 0.7664 (t70) REVERT: K 228 MET cc_start: 0.8310 (mmt) cc_final: 0.7999 (mmt) REVERT: K 245 MET cc_start: 0.8418 (mtm) cc_final: 0.7963 (mpp) REVERT: K 344 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8395 (mm-30) outliers start: 74 outliers final: 48 residues processed: 186 average time/residue: 0.2884 time to fit residues: 70.7735 Evaluate side-chains 177 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 118 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 120 ASP 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 182 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 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 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 344 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 354 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 = 0.4236 r_free = 0.4236 target = 0.086503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.071409 restraints weight = 44585.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.073672 restraints weight = 24697.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.075152 restraints weight = 16031.115| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.9231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9681 Z= 0.272 Angle : 0.804 16.344 13128 Z= 0.410 Chirality : 0.045 0.171 1461 Planarity : 0.007 0.094 1703 Dihedral : 11.679 94.274 1431 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 27.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 6.80 % Allowed : 26.31 % Favored : 66.89 % 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: -0.21 (0.23), residues: 1191 helix: 0.18 (0.20), residues: 574 sheet: 0.64 (0.36), residues: 189 loop : -0.78 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 21 HIS 0.015 0.002 HIS B 28 PHE 0.044 0.003 PHE B 378 TYR 0.136 0.003 TYR A 224 ARG 0.009 0.001 ARG A 105 *********************** 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 201 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 131 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: symmetry clash REVERT: B 103 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7639 (mttt) REVERT: B 122 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8018 (mtmt) REVERT: B 257 MET cc_start: 0.8964 (tpp) cc_final: 0.8565 (mmp) REVERT: A 52 PHE cc_start: 0.5733 (m-10) cc_final: 0.5419 (m-10) REVERT: A 120 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: A 132 LEU cc_start: 0.7029 (mp) cc_final: 0.6809 (mp) REVERT: A 182 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8157 (p) REVERT: A 212 ILE cc_start: 0.8192 (mm) cc_final: 0.7881 (mm) REVERT: A 220 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.5521 (pp20) REVERT: A 267 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.5820 (p90) REVERT: A 313 MET cc_start: 0.5860 (mtp) cc_final: 0.5003 (mtt) REVERT: A 317 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8085 (mp) REVERT: A 425 MET cc_start: 0.9002 (mmm) cc_final: 0.8753 (mmm) REVERT: A 432 TYR cc_start: 0.7137 (OUTLIER) cc_final: 0.5991 (t80) REVERT: K 28 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7297 (t80) REVERT: K 70 MET cc_start: 0.8004 (tpp) cc_final: 0.7560 (tpp) REVERT: K 115 MET cc_start: 0.7569 (tpt) cc_final: 0.7316 (ptt) REVERT: K 177 ASP cc_start: 0.7970 (t70) cc_final: 0.7654 (t70) REVERT: K 245 MET cc_start: 0.8366 (mtm) cc_final: 0.7908 (mpp) outliers start: 70 outliers final: 48 residues processed: 178 average time/residue: 0.2702 time to fit residues: 64.0443 Evaluate side-chains 177 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 120 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain 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 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 182 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 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 317 LEU 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 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: 9.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.0870 chunk 33 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 80 optimal weight: 0.1980 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 335 ASN ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN ** K 244 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 = 0.4231 r_free = 0.4231 target = 0.086339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.071309 restraints weight = 44801.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.073569 restraints weight = 24713.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.075059 restraints weight = 15999.006| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.9616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9681 Z= 0.266 Angle : 0.824 16.356 13128 Z= 0.418 Chirality : 0.045 0.180 1461 Planarity : 0.007 0.095 1703 Dihedral : 11.322 93.462 1428 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.77 % Favored : 97.15 % Rotamer: Outliers : 6.41 % Allowed : 27.48 % Favored : 66.12 % 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: 0.27 (0.20), residues: 576 sheet: 0.52 (0.35), residues: 197 loop : -0.84 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 21 HIS 0.022 0.002 HIS B 28 PHE 0.028 0.002 PHE K 72 TYR 0.134 0.002 TYR A 224 ARG 0.011 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 189 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 123 time to evaluate : 1.095 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: 0.8163 (OUTLIER) cc_final: 0.7658 (mttt) REVERT: B 122 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8000 (mtmt) REVERT: B 216 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7388 (mttp) REVERT: B 257 MET cc_start: 0.8989 (tpp) cc_final: 0.8493 (mmt) REVERT: A 52 PHE cc_start: 0.5638 (m-10) cc_final: 0.5284 (m-10) REVERT: A 120 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8290 (m-30) REVERT: A 132 LEU cc_start: 0.7276 (mp) cc_final: 0.6545 (mt) REVERT: A 182 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8077 (p) REVERT: A 212 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7978 (mm) REVERT: A 220 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.5338 (pp20) REVERT: A 267 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.5860 (p90) REVERT: A 313 MET cc_start: 0.5861 (mtp) cc_final: 0.4999 (mtt) REVERT: A 317 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8122 (mp) REVERT: A 425 MET cc_start: 0.8986 (mmm) cc_final: 0.8719 (mmm) REVERT: A 432 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.5979 (t80) REVERT: K 28 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7127 (t80) REVERT: K 177 ASP cc_start: 0.7914 (t70) cc_final: 0.7597 (t70) REVERT: K 228 MET cc_start: 0.8604 (mmt) cc_final: 0.8321 (mmt) REVERT: K 245 MET cc_start: 0.8533 (mtm) cc_final: 0.8075 (mpp) REVERT: K 344 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8533 (mm-30) outliers start: 66 outliers final: 47 residues processed: 167 average time/residue: 0.2744 time to fit residues: 60.9688 Evaluate side-chains 166 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 107 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 LEU 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 260 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 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 120 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 182 VAL 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 212 ILE Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 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 317 LEU Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 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 Chi-restraints excluded: chain K residue 344 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 89 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 GLN ** 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 ** K 361 ASN ** 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 = 0.4189 r_free = 0.4189 target = 0.084307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.069759 restraints weight = 45371.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.071917 restraints weight = 25276.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.073368 restraints weight = 16444.876| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.9998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 9681 Z= 0.309 Angle : 0.866 16.244 13128 Z= 0.441 Chirality : 0.046 0.194 1461 Planarity : 0.009 0.164 1703 Dihedral : 11.033 95.258 1424 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.11 % Favored : 96.81 % Rotamer: Outliers : 5.92 % Allowed : 29.03 % Favored : 65.05 % 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: -0.19 (0.23), residues: 1191 helix: 0.33 (0.20), residues: 576 sheet: 0.50 (0.37), residues: 193 loop : -0.92 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 21 HIS 0.025 0.002 HIS B 28 PHE 0.055 0.003 PHE B 378 TYR 0.136 0.003 TYR A 224 ARG 0.018 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 173 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 112 time to evaluate : 1.212 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 65 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7162 (mt) REVERT: B 103 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7626 (mttt) REVERT: B 122 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8203 (mtmt) REVERT: B 216 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7513 (mttp) REVERT: B 257 MET cc_start: 0.8994 (tpp) cc_final: 0.8540 (mmp) REVERT: B 379 LYS cc_start: 0.8702 (pttp) cc_final: 0.8262 (tppt) REVERT: A 52 PHE cc_start: 0.5800 (m-10) cc_final: 0.5467 (m-10) REVERT: A 103 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.7385 (t80) REVERT: A 120 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8311 (m-30) REVERT: A 132 LEU cc_start: 0.7594 (mp) cc_final: 0.6879 (mt) REVERT: A 154 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7859 (mmt) REVERT: A 182 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8129 (p) REVERT: A 212 ILE cc_start: 0.8322 (mm) cc_final: 0.8034 (mm) REVERT: A 220 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5449 (pp20) REVERT: A 267 PHE cc_start: 0.6775 (OUTLIER) cc_final: 0.5887 (p90) REVERT: A 313 MET cc_start: 0.6018 (mtp) cc_final: 0.5160 (mtt) REVERT: A 425 MET cc_start: 0.9190 (mmm) cc_final: 0.8894 (mmm) REVERT: A 432 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6044 (t80) REVERT: K 28 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.7083 (t80) REVERT: K 115 MET cc_start: 0.7354 (tmm) cc_final: 0.6675 (ptp) REVERT: K 177 ASP cc_start: 0.7908 (t70) cc_final: 0.7595 (t70) REVERT: K 228 MET cc_start: 0.8589 (mmt) cc_final: 0.8247 (mmt) REVERT: K 239 PHE cc_start: 0.8647 (t80) cc_final: 0.8003 (t80) REVERT: K 304 GLU cc_start: 0.8824 (tp30) cc_final: 0.8510 (tm-30) REVERT: K 344 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8512 (mm-30) outliers start: 61 outliers final: 44 residues processed: 154 average time/residue: 0.2696 time to fit residues: 55.7555 Evaluate side-chains 163 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 106 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 6 HIS Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 65 LEU 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 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 260 PHE Chi-restraints excluded: chain B residue 274 THR 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 422 TYR 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 103 TYR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 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 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 344 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 0.0270 chunk 24 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.085230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.070396 restraints weight = 45524.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.072631 restraints weight = 25070.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.074129 restraints weight = 16241.931| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 1.0263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 9681 Z= 0.311 Angle : 0.882 16.284 13128 Z= 0.450 Chirality : 0.046 0.203 1461 Planarity : 0.008 0.205 1703 Dihedral : 10.930 93.820 1424 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.85 % Favored : 97.06 % Rotamer: Outliers : 5.34 % Allowed : 29.22 % 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: -0.21 (0.23), residues: 1191 helix: 0.35 (0.21), residues: 573 sheet: 0.44 (0.37), residues: 196 loop : -0.97 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 21 HIS 0.023 0.002 HIS B 28 PHE 0.025 0.002 PHE B 260 TYR 0.133 0.002 TYR A 224 ARG 0.008 0.001 ARG B 380 ********************** 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 169 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 114 time to evaluate : 1.245 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: 0.8144 (OUTLIER) cc_final: 0.7569 (mttt) REVERT: B 122 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8226 (mtmt) REVERT: B 257 MET cc_start: 0.8969 (tpp) cc_final: 0.8563 (mmp) REVERT: B 379 LYS cc_start: 0.8716 (pttp) cc_final: 0.8323 (tppt) REVERT: A 132 LEU cc_start: 0.7628 (mp) cc_final: 0.7004 (mt) REVERT: A 212 ILE cc_start: 0.8274 (mm) cc_final: 0.7994 (mm) REVERT: A 220 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5396 (pp20) REVERT: A 267 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.5809 (p90) REVERT: A 313 MET cc_start: 0.6078 (mtp) cc_final: 0.5251 (mtt) REVERT: A 425 MET cc_start: 0.9153 (mmm) cc_final: 0.8848 (mmm) REVERT: A 432 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.5965 (t80) REVERT: K 28 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.6012 (t80) REVERT: K 101 ILE cc_start: 0.9252 (mm) cc_final: 0.9001 (mp) REVERT: K 115 MET cc_start: 0.7208 (tmm) cc_final: 0.6417 (ptp) REVERT: K 177 ASP cc_start: 0.7841 (t70) cc_final: 0.7535 (t70) REVERT: K 228 MET cc_start: 0.8597 (mmt) cc_final: 0.8252 (mmt) REVERT: K 239 PHE cc_start: 0.8607 (t80) cc_final: 0.8032 (t80) REVERT: K 245 MET cc_start: 0.8438 (mtm) cc_final: 0.8232 (mpp) REVERT: K 304 GLU cc_start: 0.8852 (tp30) cc_final: 0.8525 (tm-30) REVERT: K 344 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8511 (mm-30) outliers start: 55 outliers final: 43 residues processed: 152 average time/residue: 0.2582 time to fit residues: 53.4194 Evaluate side-chains 155 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 105 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 6 HIS Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 274 THR 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 422 TYR 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 136 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 182 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 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 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 344 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 101 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.083876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.069288 restraints weight = 45331.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.071408 restraints weight = 25472.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.072773 restraints weight = 16720.769| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 1.0557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9681 Z= 0.300 Angle : 0.875 16.184 13128 Z= 0.445 Chirality : 0.047 0.209 1461 Planarity : 0.010 0.287 1703 Dihedral : 10.763 95.352 1418 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 4.95 % Allowed : 29.61 % Favored : 65.44 % Cbeta Deviations : 0.00 % 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: -0.30 (0.23), residues: 1191 helix: 0.32 (0.21), residues: 582 sheet: 0.38 (0.38), residues: 187 loop : -1.08 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 21 HIS 0.021 0.002 HIS B 28 PHE 0.050 0.003 PHE B 378 TYR 0.134 0.003 TYR A 224 ARG 0.018 0.001 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4113.45 seconds wall clock time: 75 minutes 2.96 seconds (4502.96 seconds total)