Starting phenix.real_space_refine on Wed Sep 17 16:26:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ta3_10421/09_2025/6ta3_10421.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ta3_10421/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ta3_10421/09_2025/6ta3_10421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ta3_10421/09_2025/6ta3_10421.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ta3_10421/09_2025/6ta3_10421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ta3_10421/09_2025/6ta3_10421.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5952 2.51 5 N 1637 2.21 5 O 1833 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9491 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3372 Classifications: {'peptide': 429} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Chain: "A" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3425 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 415} Chain: "K" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2607 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 322} Chain breaks: 2 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'MZK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.54, per 1000 atoms: 0.27 Number of scatterers: 9491 At special positions: 0 Unit cell: (70.85, 103.55, 111.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 P 6 15.00 Mg 2 11.99 F 3 9.00 O 1833 8.00 N 1637 7.00 C 5952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 375.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.584A pdb=" N GLY B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 51 Processing helix chain 'B' and resid 69 through 79 removed outlier: 3.932A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 127 removed outlier: 4.282A pdb=" N ALA B 110 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.567A pdb=" N LEU B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR B 159 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 196 removed outlier: 4.045A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 216 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.618A pdb=" N VAL B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.514A pdb=" N LEU B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.539A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 392 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.782A pdb=" N GLU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.597A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.813A pdb=" N GLN A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 129 removed outlier: 4.339A pdb=" N GLU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 Processing helix chain 'A' and resid 181 through 198 removed outlier: 4.027A pdb=" N TYR A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 223 through 244 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.677A pdb=" N GLU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 381 through 402 removed outlier: 3.890A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 412 removed outlier: 3.795A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 Processing helix chain 'K' and resid 29 through 36 Processing helix chain 'K' and resid 77 through 96 removed outlier: 3.695A pdb=" N CYS K 87 " --> pdb=" O ARG K 83 " (cutoff:3.500A) Proline residue: K 88 - end of helix removed outlier: 3.503A pdb=" N GLU K 92 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 117 removed outlier: 3.549A pdb=" N GLY K 117 " --> pdb=" O PHE K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 151 removed outlier: 3.601A pdb=" N LEU K 140 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS K 141 " --> pdb=" O PRO K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 222 removed outlier: 4.247A pdb=" N VAL K 210 " --> pdb=" O ASN K 206 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA K 219 " --> pdb=" O GLU K 215 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS K 220 " --> pdb=" O LYS K 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 276 Processing helix chain 'K' and resid 278 through 305 Processing helix chain 'K' and resid 310 through 313 Processing helix chain 'K' and resid 314 through 320 Processing helix chain 'K' and resid 321 through 324 Processing helix chain 'K' and resid 342 through 359 removed outlier: 3.549A pdb=" N THR K 346 " --> pdb=" O ASN K 342 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS K 357 " --> pdb=" O ALA K 353 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN K 358 " --> pdb=" O HIS K 354 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE K 359 " --> pdb=" O ARG K 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 65 removed outlier: 5.873A pdb=" N VAL B 5 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N THR B 136 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE B 7 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N SER B 138 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 267 through 270 removed outlier: 3.527A pdb=" N GLY B 369 " --> pdb=" O MET B 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 314 through 317 Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 67 removed outlier: 5.661A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 273 Processing sheet with id=AA8, first strand: chain 'K' and resid 70 through 72 removed outlier: 3.669A pdb=" N MET K 70 " --> pdb=" O VAL K 21 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN K 98 " --> pdb=" O ARG K 329 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER K 331 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR K 100 " --> pdb=" O SER K 331 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE K 333 " --> pdb=" O THR K 100 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE K 102 " --> pdb=" O ILE K 333 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR K 335 " --> pdb=" O PHE K 102 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR K 104 " --> pdb=" O THR K 335 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 70 through 72 removed outlier: 3.669A pdb=" N MET K 70 " --> pdb=" O VAL K 21 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN K 98 " --> pdb=" O ARG K 329 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER K 331 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR K 100 " --> pdb=" O SER K 331 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE K 333 " --> pdb=" O THR K 100 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE K 102 " --> pdb=" O ILE K 333 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR K 335 " --> pdb=" O PHE K 102 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR K 104 " --> pdb=" O THR K 335 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL K 158 " --> pdb=" O ILE K 202 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE K 202 " --> pdb=" O VAL K 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 42 through 44 Processing sheet with id=AB2, first strand: chain 'K' and resid 183 through 187 removed outlier: 4.264A pdb=" N GLN K 183 " --> pdb=" O LYS K 197 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLY K 193 " --> pdb=" O ASP K 187 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.91: 1 0.91 - 1.14: 3 1.14 - 1.36: 3087 1.36 - 1.59: 6495 1.59 - 1.82: 95 Bond restraints: 9681 Sorted by residual: bond pdb=" CB SER K 84 " pdb=" OG SER K 84 " ideal model delta sigma weight residual 1.417 0.678 0.739 2.00e-02 2.50e+03 1.37e+03 bond pdb=" CB GLU K 254 " pdb=" CG GLU K 254 " ideal model delta sigma weight residual 1.520 1.061 0.459 3.00e-02 1.11e+03 2.35e+02 bond pdb=" C3A G2P A 501 " pdb=" PB G2P A 501 " ideal model delta sigma weight residual 1.850 1.591 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C THR K 306 " pdb=" O THR K 306 " ideal model delta sigma weight residual 1.234 1.083 0.151 1.26e-02 6.30e+03 1.43e+02 bond pdb=" C3A G2P A 501 " pdb=" PA G2P A 501 " ideal model delta sigma weight residual 1.818 1.592 0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 9676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.76: 12991 6.76 - 13.52: 125 13.52 - 20.28: 6 20.28 - 27.04: 3 27.04 - 33.80: 3 Bond angle restraints: 13128 Sorted by residual: angle pdb=" CA GLY B 10 " pdb=" C GLY B 10 " pdb=" N GLN B 11 " ideal model delta sigma weight residual 115.13 148.93 -33.80 1.05e+00 9.07e-01 1.04e+03 angle pdb=" O GLY B 10 " pdb=" C GLY B 10 " pdb=" N GLN B 11 " ideal model delta sigma weight residual 122.56 90.86 31.70 1.15e+00 7.56e-01 7.60e+02 angle pdb=" CA SER K 84 " pdb=" CB SER K 84 " pdb=" OG SER K 84 " ideal model delta sigma weight residual 111.10 139.29 -28.19 2.00e+00 2.50e-01 1.99e+02 angle pdb=" CA GLU K 254 " pdb=" CB GLU K 254 " pdb=" CG GLU K 254 " ideal model delta sigma weight residual 114.10 139.62 -25.52 2.00e+00 2.50e-01 1.63e+02 angle pdb=" N ASN K 289 " pdb=" CA ASN K 289 " pdb=" C ASN K 289 " ideal model delta sigma weight residual 111.07 99.23 11.84 1.07e+00 8.73e-01 1.22e+02 ... (remaining 13123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.36: 5060 18.36 - 36.72: 507 36.72 - 55.08: 182 55.08 - 73.44: 86 73.44 - 91.80: 15 Dihedral angle restraints: 5850 sinusoidal: 2385 harmonic: 3465 Sorted by residual: dihedral pdb=" CA GLY K 110 " pdb=" C GLY K 110 " pdb=" N LYS K 111 " pdb=" CA LYS K 111 " ideal model delta harmonic sigma weight residual 180.00 137.42 42.58 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" CA GLN B 15 " pdb=" C GLN B 15 " pdb=" N ILE B 16 " pdb=" CA ILE B 16 " ideal model delta harmonic sigma weight residual -180.00 -146.07 -33.93 0 5.00e+00 4.00e-02 4.61e+01 dihedral pdb=" N THR B 143 " pdb=" C THR B 143 " pdb=" CA THR B 143 " pdb=" CB THR B 143 " ideal model delta harmonic sigma weight residual 123.40 138.49 -15.09 0 2.50e+00 1.60e-01 3.64e+01 ... (remaining 5847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 1413 0.183 - 0.365: 43 0.365 - 0.548: 3 0.548 - 0.731: 1 0.731 - 0.913: 1 Chirality restraints: 1461 Sorted by residual: chirality pdb=" CG LEU K 266 " pdb=" CB LEU K 266 " pdb=" CD1 LEU K 266 " pdb=" CD2 LEU K 266 " both_signs ideal model delta sigma weight residual False -2.59 -1.68 -0.91 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" CA THR B 143 " pdb=" N THR B 143 " pdb=" C THR B 143 " pdb=" CB THR B 143 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA PRO K 137 " pdb=" N PRO K 137 " pdb=" C PRO K 137 " pdb=" CB PRO K 137 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.48 2.00e-01 2.50e+01 5.87e+00 ... (remaining 1458 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 399 " -0.268 2.00e-02 2.50e+03 1.90e-01 7.21e+02 pdb=" CG TYR A 399 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 399 " 0.091 2.00e-02 2.50e+03 pdb=" CD2 TYR A 399 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 TYR A 399 " 0.170 2.00e-02 2.50e+03 pdb=" CE2 TYR A 399 " 0.155 2.00e-02 2.50e+03 pdb=" CZ TYR A 399 " 0.109 2.00e-02 2.50e+03 pdb=" OH TYR A 399 " -0.369 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 345 " -0.043 2.00e-02 2.50e+03 9.65e-02 9.30e+01 pdb=" CD GLU K 345 " 0.167 2.00e-02 2.50e+03 pdb=" OE1 GLU K 345 " -0.063 2.00e-02 2.50e+03 pdb=" OE2 GLU K 345 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 104 " -0.128 2.00e-02 2.50e+03 6.80e-02 9.24e+01 pdb=" CG TYR K 104 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR K 104 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR K 104 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 TYR K 104 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR K 104 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR K 104 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR K 104 " -0.085 2.00e-02 2.50e+03 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 0.44 - 1.33: 14 1.33 - 2.22: 110 2.22 - 3.12: 13174 3.12 - 4.01: 31103 4.01 - 4.90: 53116 Warning: very small nonbonded interaction distances. Nonbonded interactions: 97517 Sorted by model distance: nonbonded pdb=" OD1 ASN B 99 " pdb=" PG G2P B 501 " model vdw 0.439 2.720 nonbonded pdb=" O PRO B 259 " pdb=" CD1 PHE A 404 " model vdw 0.578 3.340 nonbonded pdb=" CD LYS B 350 " pdb=" O THR A 179 " model vdw 0.861 3.440 nonbonded pdb=" CG PHE B 260 " pdb=" CE1 HIS A 406 " model vdw 0.923 3.480 nonbonded pdb=" CE LYS B 324 " pdb=" CA ARG A 221 " model vdw 0.951 3.096 ... (remaining 97512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.560 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- 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 : 0.032 1.113 9691 Z= 2.718 Angle : 2.453 33.803 13128 Z= 1.751 Chirality : 0.078 0.913 1461 Planarity : 0.013 0.190 1703 Dihedral : 18.955 91.805 3624 Min Nonbonded Distance : 0.439 Molprobity Statistics. All-atom Clashscore : 210.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 16.02 % Allowed : 16.99 % Favored : 66.99 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.22), residues: 1191 helix: 2.57 (0.20), residues: 558 sheet: 1.18 (0.37), residues: 171 loop : -0.45 (0.23), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.086 0.002 ARG A 402 TYR 0.369 0.011 TYR A 399 PHE 0.033 0.002 PHE K 113 TRP 0.020 0.004 TRP B 344 HIS 0.004 0.000 HIS K 354 Details of bonding type rmsd covalent geometry : bond 0.02375 ( 9681) covalent geometry : angle 2.45329 (13128) hydrogen bonds : bond 0.23958 ( 499) hydrogen bonds : angle 9.07906 ( 1551) Misc. bond : bond 0.68362 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 208 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7762 (mttt) REVERT: B 210 ILE cc_start: 0.8044 (mt) cc_final: 0.7731 (mm) REVERT: B 336 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7155 (mttt) REVERT: B 359 ARG cc_start: 0.6333 (mtt180) cc_final: 0.4899 (mtt180) REVERT: A 22 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6641 (tm-30) REVERT: A 164 LYS cc_start: 0.4698 (OUTLIER) cc_final: 0.3090 (mmtp) REVERT: A 212 ILE cc_start: 0.8030 (mm) cc_final: 0.7752 (mm) REVERT: A 220 GLU cc_start: 0.3323 (OUTLIER) cc_final: 0.2572 (pp20) REVERT: A 266 HIS cc_start: 0.6925 (m90) cc_final: 0.6325 (m90) REVERT: A 303 VAL cc_start: 0.8192 (p) cc_final: 0.7285 (p) REVERT: A 396 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7719 (t0) outliers start: 165 outliers final: 67 residues processed: 337 average time/residue: 0.1396 time to fit residues: 60.2127 Evaluate side-chains 181 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 108 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 33 ARG Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 189 ARG Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 280 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN A 18 ASN A 31 GLN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS A 176 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN A 283 HIS ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.089799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.075401 restraints weight = 44422.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.077893 restraints weight = 24868.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.079530 restraints weight = 15980.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.080624 restraints weight = 11420.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.081215 restraints weight = 8893.740| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 9691 Z= 0.323 Angle : 1.064 16.379 13128 Z= 0.564 Chirality : 0.058 0.354 1461 Planarity : 0.010 0.110 1703 Dihedral : 15.597 88.358 1590 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 48.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 12.04 % Allowed : 20.97 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.22), residues: 1191 helix: -0.01 (0.19), residues: 574 sheet: 1.14 (0.37), residues: 184 loop : -0.60 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 181 TYR 0.146 0.005 TYR A 224 PHE 0.043 0.004 PHE B 260 TRP 0.011 0.003 TRP B 21 HIS 0.016 0.003 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00670 ( 9681) covalent geometry : angle 1.06429 (13128) hydrogen bonds : bond 0.08290 ( 499) hydrogen bonds : angle 7.07276 ( 1551) Misc. bond : bond 0.01515 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 161 time to evaluate : 0.423 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: B 3 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5997 (mm-30) REVERT: B 22 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6895 (pp20) REVERT: B 23 VAL cc_start: 0.8701 (p) cc_final: 0.8065 (m) REVERT: B 31 ASP cc_start: 0.3234 (OUTLIER) cc_final: 0.2920 (t0) REVERT: B 122 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.7865 (mtmt) REVERT: B 147 MET cc_start: 0.7173 (pmm) cc_final: 0.6732 (pmm) REVERT: B 154 LYS cc_start: 0.9256 (mmmt) cc_final: 0.8700 (tttp) REVERT: B 155 ILE cc_start: 0.7462 (pt) cc_final: 0.7067 (tp) REVERT: B 158 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.5883 (mp0) REVERT: B 228 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8276 (tt) REVERT: B 260 PHE cc_start: 0.4678 (OUTLIER) cc_final: 0.4468 (t80) REVERT: B 280 GLN cc_start: 0.7253 (pt0) cc_final: 0.6991 (pt0) REVERT: B 291 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8391 (pp30) REVERT: B 336 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8138 (mttt) REVERT: B 363 MET cc_start: 0.8071 (mpp) cc_final: 0.7837 (mpp) REVERT: A 41 THR cc_start: 0.4464 (OUTLIER) cc_final: 0.4221 (m) REVERT: A 52 PHE cc_start: 0.6126 (m-10) cc_final: 0.5569 (m-10) REVERT: A 86 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8703 (tp) REVERT: A 164 LYS cc_start: 0.5179 (OUTLIER) cc_final: 0.4537 (tppt) REVERT: A 204 VAL cc_start: 0.5764 (OUTLIER) cc_final: 0.5506 (p) REVERT: A 212 ILE cc_start: 0.8156 (mm) cc_final: 0.7809 (mm) REVERT: A 220 GLU cc_start: 0.4616 (OUTLIER) cc_final: 0.3250 (pp20) REVERT: A 242 LEU cc_start: 0.5871 (OUTLIER) cc_final: 0.5537 (tm) REVERT: A 338 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8005 (tppp) REVERT: A 371 VAL cc_start: 0.3894 (OUTLIER) cc_final: 0.3683 (t) REVERT: K 101 ILE cc_start: 0.9249 (mt) cc_final: 0.9021 (tp) REVERT: K 177 ASP cc_start: 0.7705 (t70) cc_final: 0.7351 (t70) REVERT: K 184 MET cc_start: 0.7072 (tmm) cc_final: 0.6799 (tmm) REVERT: K 245 MET cc_start: 0.8141 (mtm) cc_final: 0.7926 (mtm) REVERT: K 261 LEU cc_start: 0.9354 (tp) cc_final: 0.9081 (tp) REVERT: K 263 LEU cc_start: 0.8871 (mm) cc_final: 0.8301 (mt) REVERT: K 290 GLN cc_start: 0.8780 (pp30) cc_final: 0.8203 (pt0) outliers start: 124 outliers final: 49 residues processed: 256 average time/residue: 0.1377 time to fit residues: 45.8095 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 : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 228 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 273 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 41 THR 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 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 311 LYS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain K residue 33 ARG Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain K residue 342 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 95 optimal weight: 0.0010 chunk 102 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 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 393 HIS ** K 244 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 = 0.4265 r_free = 0.4265 target = 0.088035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.073221 restraints weight = 44796.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.075554 restraints weight = 25607.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.077098 restraints weight = 16728.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.078184 restraints weight = 12145.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.078893 restraints weight = 9539.436| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.7045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9691 Z= 0.237 Angle : 0.890 16.262 13128 Z= 0.463 Chirality : 0.050 0.345 1461 Planarity : 0.008 0.088 1703 Dihedral : 13.464 90.912 1497 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 35.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.60 % Favored : 97.31 % Rotamer: Outliers : 9.22 % Allowed : 22.52 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.22), residues: 1191 helix: -0.01 (0.20), residues: 571 sheet: 0.60 (0.36), residues: 189 loop : -0.80 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 156 TYR 0.148 0.003 TYR A 224 PHE 0.028 0.003 PHE A 267 TRP 0.031 0.004 TRP B 101 HIS 0.010 0.002 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 9681) covalent geometry : angle 0.89035 (13128) hydrogen bonds : bond 0.06710 ( 499) hydrogen bonds : angle 6.46376 ( 1551) Misc. bond : bond 0.01527 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 140 time to evaluate : 0.402 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: 0.6116 (OUTLIER) cc_final: 0.5578 (mm-30) REVERT: B 22 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6609 (pt0) REVERT: B 122 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8009 (mtmt) REVERT: B 155 ILE cc_start: 0.7801 (pt) cc_final: 0.7412 (mm) REVERT: B 156 ARG cc_start: 0.7734 (tpt90) cc_final: 0.6904 (tpp80) REVERT: B 270 PHE cc_start: 0.6736 (t80) cc_final: 0.6310 (t80) REVERT: B 280 GLN cc_start: 0.7121 (pt0) cc_final: 0.6832 (pt0) REVERT: B 293 MET cc_start: 0.7464 (mmt) cc_final: 0.6215 (ppp) REVERT: B 331 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8303 (pp) REVERT: B 336 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8246 (mttt) REVERT: B 376 GLU cc_start: 0.5025 (OUTLIER) cc_final: 0.4462 (mp0) REVERT: B 379 LYS cc_start: 0.8477 (pttp) cc_final: 0.8246 (pttp) REVERT: A 52 PHE cc_start: 0.6251 (m-10) cc_final: 0.5845 (m-10) REVERT: A 205 ASP cc_start: 0.6466 (OUTLIER) cc_final: 0.5714 (m-30) REVERT: A 209 ILE cc_start: 0.7468 (mt) cc_final: 0.7224 (mt) REVERT: A 212 ILE cc_start: 0.8150 (mm) cc_final: 0.7837 (mm) REVERT: A 242 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.5194 (tm) REVERT: A 267 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.5733 (p90) REVERT: A 311 LYS cc_start: 0.6858 (OUTLIER) cc_final: 0.6582 (mppt) REVERT: A 432 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.5792 (t80) REVERT: K 177 ASP cc_start: 0.7857 (t70) cc_final: 0.7515 (t70) REVERT: K 290 GLN cc_start: 0.8889 (pp30) cc_final: 0.8337 (pt0) REVERT: K 367 GLN cc_start: 0.6527 (OUTLIER) cc_final: 0.5796 (tp-100) outliers start: 95 outliers final: 44 residues processed: 210 average time/residue: 0.1285 time to fit residues: 35.6335 Evaluate side-chains 172 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 116 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 22 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 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 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 33 ARG Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 367 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN B 134 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 279 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.086403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.071750 restraints weight = 44852.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.073963 restraints weight = 25191.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.075447 restraints weight = 16382.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.076443 restraints weight = 11889.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.077112 restraints weight = 9428.540| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.7888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9691 Z= 0.215 Angle : 0.867 20.831 13128 Z= 0.443 Chirality : 0.046 0.191 1461 Planarity : 0.008 0.166 1703 Dihedral : 12.589 82.988 1457 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 32.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 8.25 % Allowed : 23.59 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.22), residues: 1191 helix: 0.06 (0.20), residues: 572 sheet: 0.38 (0.36), residues: 193 loop : -0.99 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 241 TYR 0.143 0.003 TYR A 224 PHE 0.025 0.003 PHE B 260 TRP 0.032 0.003 TRP B 21 HIS 0.017 0.002 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 9681) covalent geometry : angle 0.86687 (13128) hydrogen bonds : bond 0.06161 ( 499) hydrogen bonds : angle 6.19911 ( 1551) Misc. bond : bond 0.01538 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 126 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7595 (mttt) REVERT: B 114 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8132 (t0) REVERT: B 122 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8111 (mtmt) REVERT: B 233 MET cc_start: 0.7055 (mtp) cc_final: 0.6055 (tpp) REVERT: B 286 VAL cc_start: 0.7647 (OUTLIER) cc_final: 0.7395 (t) REVERT: B 293 MET cc_start: 0.7508 (mmt) cc_final: 0.6331 (ppp) REVERT: B 331 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8188 (pp) REVERT: B 336 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8263 (mttt) REVERT: B 379 LYS cc_start: 0.8503 (pttp) cc_final: 0.8170 (pttp) REVERT: A 52 PHE cc_start: 0.5912 (m-10) cc_final: 0.5287 (m-10) REVERT: A 212 ILE cc_start: 0.8239 (mm) cc_final: 0.7916 (mm) REVERT: A 220 GLU cc_start: 0.5862 (OUTLIER) cc_final: 0.5338 (pp20) REVERT: A 242 LEU cc_start: 0.5515 (OUTLIER) cc_final: 0.5198 (tm) REVERT: A 267 PHE cc_start: 0.6625 (OUTLIER) cc_final: 0.5590 (p90) REVERT: A 311 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6712 (mppt) REVERT: A 313 MET cc_start: 0.5839 (mtp) cc_final: 0.5023 (mtt) REVERT: A 425 MET cc_start: 0.9136 (mmm) cc_final: 0.8847 (mmm) REVERT: A 432 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.5959 (t80) REVERT: K 177 ASP cc_start: 0.7852 (t70) cc_final: 0.7515 (t70) REVERT: K 181 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.6066 (tmt170) REVERT: K 239 PHE cc_start: 0.8492 (t80) cc_final: 0.8060 (t80) REVERT: K 245 MET cc_start: 0.8382 (mtm) cc_final: 0.7892 (mpp) REVERT: K 290 GLN cc_start: 0.8798 (pp30) cc_final: 0.8372 (pt0) REVERT: K 367 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.5648 (tm-30) outliers start: 85 outliers final: 42 residues processed: 190 average time/residue: 0.1162 time to fit residues: 29.8892 Evaluate side-chains 167 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 112 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 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 209 ILE Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 237 SER Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 367 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 46 optimal weight: 0.4980 chunk 116 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 11 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN A 61 HIS ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.086126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.071270 restraints weight = 44684.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.073512 restraints weight = 24984.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.074926 restraints weight = 16230.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.075911 restraints weight = 11878.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.076512 restraints weight = 9468.767| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.8544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 9691 Z= 0.199 Angle : 0.829 16.087 13128 Z= 0.421 Chirality : 0.046 0.180 1461 Planarity : 0.007 0.086 1703 Dihedral : 12.173 92.669 1448 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 29.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 7.38 % Allowed : 24.66 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.23), residues: 1191 helix: 0.11 (0.20), residues: 591 sheet: 0.23 (0.36), residues: 193 loop : -0.85 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG B 251 TYR 0.141 0.003 TYR A 224 PHE 0.022 0.002 PHE B 260 TRP 0.019 0.002 TRP B 21 HIS 0.016 0.002 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9681) covalent geometry : angle 0.82852 (13128) hydrogen bonds : bond 0.05842 ( 499) hydrogen bonds : angle 5.98346 ( 1551) Misc. bond : bond 0.01552 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 129 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7874 (mttp) REVERT: B 114 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8126 (t0) REVERT: B 122 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8088 (mtmt) REVERT: B 212 PHE cc_start: 0.7793 (t80) cc_final: 0.7583 (t80) REVERT: B 257 MET cc_start: 0.8766 (tpp) cc_final: 0.8448 (mmp) REVERT: B 270 PHE cc_start: 0.6551 (t80) cc_final: 0.5938 (t80) REVERT: B 293 MET cc_start: 0.7606 (mmt) cc_final: 0.6453 (ppp) REVERT: B 331 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8198 (pp) REVERT: B 336 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8213 (mtmm) REVERT: B 379 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8147 (pttp) REVERT: A 52 PHE cc_start: 0.6004 (m-10) cc_final: 0.5582 (m-10) REVERT: A 203 MET cc_start: 0.6355 (mpp) cc_final: 0.5748 (mpp) REVERT: A 209 ILE cc_start: 0.7803 (mt) cc_final: 0.7462 (mt) REVERT: A 212 ILE cc_start: 0.8293 (mm) cc_final: 0.7991 (mm) REVERT: A 220 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.5505 (pp20) REVERT: A 242 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.5149 (tm) REVERT: A 267 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.5374 (p90) REVERT: A 308 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6778 (mpt180) REVERT: A 311 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6793 (mppt) REVERT: A 313 MET cc_start: 0.5867 (mtp) cc_final: 0.5046 (mtt) REVERT: A 425 MET cc_start: 0.9008 (mmm) cc_final: 0.8715 (mmm) REVERT: A 432 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.5955 (t80) REVERT: K 70 MET cc_start: 0.7935 (tpp) cc_final: 0.7630 (tpp) REVERT: K 177 ASP cc_start: 0.7985 (t70) cc_final: 0.7662 (t70) REVERT: K 239 PHE cc_start: 0.8724 (t80) cc_final: 0.8209 (t80) REVERT: K 245 MET cc_start: 0.8394 (mtm) cc_final: 0.8010 (mpp) REVERT: K 367 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.5725 (tm-30) outliers start: 76 outliers final: 45 residues processed: 183 average time/residue: 0.1159 time to fit residues: 28.7189 Evaluate side-chains 176 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 118 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 276 ARG 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 376 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain A residue 41 THR 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 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 367 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 10 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 70 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN B 226 ASN ** B 245 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.084944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.070117 restraints weight = 44562.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.072278 restraints weight = 25215.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.073708 restraints weight = 16553.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.074659 restraints weight = 12147.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.075274 restraints weight = 9724.313| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.8948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9691 Z= 0.195 Angle : 0.809 16.168 13128 Z= 0.414 Chirality : 0.046 0.323 1461 Planarity : 0.007 0.092 1703 Dihedral : 11.912 93.677 1441 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 29.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 6.99 % Allowed : 25.34 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.23), residues: 1191 helix: 0.15 (0.19), residues: 591 sheet: 0.20 (0.36), residues: 194 loop : -0.89 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 251 TYR 0.139 0.003 TYR A 224 PHE 0.033 0.003 PHE B 260 TRP 0.013 0.002 TRP B 21 HIS 0.015 0.002 HIS K 236 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9681) covalent geometry : angle 0.80934 (13128) hydrogen bonds : bond 0.05777 ( 499) hydrogen bonds : angle 5.84876 ( 1551) Misc. bond : bond 0.01525 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 120 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7651 (mttt) REVERT: B 122 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8069 (mtmt) REVERT: B 257 MET cc_start: 0.8803 (tpp) cc_final: 0.8467 (mmp) REVERT: B 270 PHE cc_start: 0.6430 (t80) cc_final: 0.5929 (t80) REVERT: B 293 MET cc_start: 0.7763 (mmt) cc_final: 0.6652 (ppp) REVERT: B 331 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8060 (pp) REVERT: B 336 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8120 (mttt) REVERT: B 379 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8210 (pttp) REVERT: A 52 PHE cc_start: 0.5884 (m-10) cc_final: 0.5551 (m-10) REVERT: A 188 ILE cc_start: 0.7350 (mp) cc_final: 0.7145 (mt) REVERT: A 203 MET cc_start: 0.6669 (mpp) cc_final: 0.6307 (mpp) REVERT: A 212 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7863 (mm) REVERT: A 220 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.5520 (pp20) REVERT: A 242 LEU cc_start: 0.5473 (OUTLIER) cc_final: 0.5200 (tm) REVERT: A 267 PHE cc_start: 0.6498 (OUTLIER) cc_final: 0.5394 (p90) REVERT: A 313 MET cc_start: 0.5857 (mtp) cc_final: 0.5197 (mtt) REVERT: A 373 ARG cc_start: 0.7084 (mpt180) cc_final: 0.6851 (mtt180) REVERT: A 425 MET cc_start: 0.9060 (mmm) cc_final: 0.8778 (mmm) REVERT: A 432 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.5954 (t80) REVERT: K 70 MET cc_start: 0.8076 (tpp) cc_final: 0.7847 (tpp) REVERT: K 177 ASP cc_start: 0.7934 (t70) cc_final: 0.7594 (t70) REVERT: K 245 MET cc_start: 0.8453 (mtm) cc_final: 0.8056 (mpp) REVERT: K 367 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.5720 (tm-30) outliers start: 72 outliers final: 52 residues processed: 169 average time/residue: 0.1154 time to fit residues: 26.1212 Evaluate side-chains 176 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 113 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 331 LEU 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 5 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 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 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 367 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 82 optimal weight: 0.0980 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.085163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.070243 restraints weight = 44743.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.072400 restraints weight = 25705.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.073807 restraints weight = 17014.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.074803 restraints weight = 12565.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.075499 restraints weight = 10005.441| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.9255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9691 Z= 0.188 Angle : 0.820 18.079 13128 Z= 0.412 Chirality : 0.046 0.274 1461 Planarity : 0.007 0.093 1703 Dihedral : 12.125 94.517 1437 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 27.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 7.38 % Allowed : 25.92 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.23), residues: 1191 helix: 0.23 (0.20), residues: 578 sheet: 0.09 (0.36), residues: 194 loop : -0.83 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 251 TYR 0.180 0.003 TYR A 224 PHE 0.054 0.003 PHE B 167 TRP 0.011 0.002 TRP B 21 HIS 0.020 0.002 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9681) covalent geometry : angle 0.81982 (13128) hydrogen bonds : bond 0.05590 ( 499) hydrogen bonds : angle 5.75993 ( 1551) Misc. bond : bond 0.01804 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 127 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7634 (mttt) REVERT: B 122 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8041 (mtmt) REVERT: B 257 MET cc_start: 0.8770 (tpp) cc_final: 0.8493 (mmp) REVERT: B 270 PHE cc_start: 0.6393 (t80) cc_final: 0.5944 (t80) REVERT: B 293 MET cc_start: 0.7767 (mmt) cc_final: 0.6577 (ppp) REVERT: A 52 PHE cc_start: 0.5859 (m-10) cc_final: 0.5587 (m-10) REVERT: A 212 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7885 (mm) REVERT: A 220 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.5439 (pp20) REVERT: A 242 LEU cc_start: 0.5452 (OUTLIER) cc_final: 0.5212 (tm) REVERT: A 267 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.5424 (p90) REVERT: A 308 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6584 (mpt180) REVERT: A 313 MET cc_start: 0.5799 (mtp) cc_final: 0.5155 (mtt) REVERT: A 373 ARG cc_start: 0.7071 (mpt180) cc_final: 0.6845 (mtt180) REVERT: A 425 MET cc_start: 0.9138 (mmm) cc_final: 0.8850 (mmm) REVERT: A 432 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.5961 (t80) REVERT: K 70 MET cc_start: 0.8077 (tpp) cc_final: 0.7871 (tpp) REVERT: K 177 ASP cc_start: 0.7911 (t70) cc_final: 0.7568 (t70) REVERT: K 239 PHE cc_start: 0.8661 (t80) cc_final: 0.8122 (t80) REVERT: K 245 MET cc_start: 0.8469 (mtm) cc_final: 0.8073 (mpp) REVERT: K 367 GLN cc_start: 0.6808 (OUTLIER) cc_final: 0.5723 (tm-30) outliers start: 76 outliers final: 50 residues processed: 182 average time/residue: 0.1271 time to fit residues: 30.3977 Evaluate side-chains 172 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 113 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 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 B residue 379 LYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 367 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 59 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN ** B 291 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 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.084542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.069799 restraints weight = 44892.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.071959 restraints weight = 25471.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.073364 restraints weight = 16687.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.074296 restraints weight = 12248.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.074965 restraints weight = 9787.790| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.9697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9691 Z= 0.199 Angle : 0.851 19.533 13128 Z= 0.427 Chirality : 0.047 0.272 1461 Planarity : 0.010 0.278 1703 Dihedral : 11.937 95.728 1429 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 28.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 6.60 % Allowed : 26.02 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.23), residues: 1191 helix: 0.30 (0.20), residues: 580 sheet: 0.03 (0.35), residues: 194 loop : -0.77 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 251 TYR 0.184 0.003 TYR A 224 PHE 0.038 0.003 PHE B 260 TRP 0.009 0.002 TRP B 21 HIS 0.017 0.002 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9681) covalent geometry : angle 0.85148 (13128) hydrogen bonds : bond 0.05615 ( 499) hydrogen bonds : angle 5.69282 ( 1551) Misc. bond : bond 0.01735 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 116 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7642 (mttt) REVERT: B 122 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8124 (mtmt) REVERT: B 257 MET cc_start: 0.8819 (tpp) cc_final: 0.8529 (mmp) REVERT: B 270 PHE cc_start: 0.6444 (t80) cc_final: 0.5984 (t80) REVERT: B 293 MET cc_start: 0.7833 (mmt) cc_final: 0.6813 (ppp) REVERT: A 52 PHE cc_start: 0.5780 (m-10) cc_final: 0.5439 (m-10) REVERT: A 149 PHE cc_start: 0.7281 (t80) cc_final: 0.6986 (m-80) REVERT: A 203 MET cc_start: 0.6848 (mpp) cc_final: 0.6143 (mpp) REVERT: A 212 ILE cc_start: 0.8160 (mm) cc_final: 0.7856 (mm) REVERT: A 220 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5497 (pp20) REVERT: A 267 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.5488 (p90) REVERT: A 308 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6764 (mpt180) REVERT: A 313 MET cc_start: 0.6171 (mtp) cc_final: 0.5362 (mtt) REVERT: A 373 ARG cc_start: 0.7273 (mpt180) cc_final: 0.6834 (mtt180) REVERT: A 396 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8034 (t0) REVERT: A 425 MET cc_start: 0.9163 (mmm) cc_final: 0.8864 (mmm) REVERT: A 432 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.5990 (t80) REVERT: K 70 MET cc_start: 0.8123 (tpp) cc_final: 0.7708 (tpp) REVERT: K 115 MET cc_start: 0.8078 (tpp) cc_final: 0.7682 (ptt) REVERT: K 177 ASP cc_start: 0.7877 (t70) cc_final: 0.7544 (t70) REVERT: K 228 MET cc_start: 0.8452 (mmp) cc_final: 0.8012 (mmt) REVERT: K 239 PHE cc_start: 0.8755 (t80) cc_final: 0.8233 (t80) REVERT: K 245 MET cc_start: 0.8380 (mtm) cc_final: 0.8043 (mpp) REVERT: K 367 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.5798 (tm-30) outliers start: 68 outliers final: 48 residues processed: 168 average time/residue: 0.1258 time to fit residues: 27.9803 Evaluate side-chains 167 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 111 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 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 272 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 367 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.082155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.067592 restraints weight = 45596.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.069630 restraints weight = 25767.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.070977 restraints weight = 16972.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.071876 restraints weight = 12522.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.072497 restraints weight = 10056.021| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 1.0136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9691 Z= 0.222 Angle : 0.855 18.001 13128 Z= 0.437 Chirality : 0.047 0.243 1461 Planarity : 0.010 0.265 1703 Dihedral : 11.760 97.546 1429 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 28.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.02 % Allowed : 26.99 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.23), residues: 1191 helix: 0.43 (0.20), residues: 578 sheet: -0.11 (0.37), residues: 192 loop : -0.96 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 276 TYR 0.179 0.003 TYR A 224 PHE 0.035 0.003 PHE B 167 TRP 0.010 0.002 TRP A 21 HIS 0.025 0.003 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 9681) covalent geometry : angle 0.85450 (13128) hydrogen bonds : bond 0.05793 ( 499) hydrogen bonds : angle 5.66659 ( 1551) Misc. bond : bond 0.01675 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 120 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8254 (mtmt) REVERT: B 257 MET cc_start: 0.8899 (tpp) cc_final: 0.8500 (mmp) REVERT: B 270 PHE cc_start: 0.7163 (t80) cc_final: 0.6624 (t80) REVERT: B 293 MET cc_start: 0.8116 (mmt) cc_final: 0.6773 (ppp) REVERT: A 52 PHE cc_start: 0.5794 (m-10) cc_final: 0.5553 (m-10) REVERT: A 203 MET cc_start: 0.7389 (mpp) cc_final: 0.6525 (mpp) REVERT: A 212 ILE cc_start: 0.8253 (mm) cc_final: 0.7974 (mm) REVERT: A 220 GLU cc_start: 0.6186 (OUTLIER) cc_final: 0.5584 (pp20) REVERT: A 267 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.5646 (p90) REVERT: A 308 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6979 (mpt180) REVERT: A 313 MET cc_start: 0.6382 (mtp) cc_final: 0.5535 (mtt) REVERT: A 373 ARG cc_start: 0.7608 (mpt180) cc_final: 0.7040 (mtt180) REVERT: A 432 TYR cc_start: 0.7262 (OUTLIER) cc_final: 0.6068 (t80) REVERT: K 115 MET cc_start: 0.8220 (tpp) cc_final: 0.7855 (ptp) REVERT: K 177 ASP cc_start: 0.7906 (t70) cc_final: 0.7571 (t70) REVERT: K 215 GLU cc_start: 0.5351 (OUTLIER) cc_final: 0.4905 (pm20) REVERT: K 245 MET cc_start: 0.8467 (mtm) cc_final: 0.7944 (mpp) REVERT: K 367 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.5881 (tm-30) outliers start: 62 outliers final: 45 residues processed: 170 average time/residue: 0.1231 time to fit residues: 27.8528 Evaluate side-chains 159 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 107 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 367 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 99 optimal weight: 0.0670 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 13 optimal weight: 0.0970 chunk 117 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 279 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.083927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.069134 restraints weight = 45049.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.071191 restraints weight = 25518.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.072571 restraints weight = 16853.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.073464 restraints weight = 12463.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.074026 restraints weight = 10044.127| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 1.0440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9691 Z= 0.182 Angle : 0.859 17.724 13128 Z= 0.433 Chirality : 0.046 0.258 1461 Planarity : 0.011 0.345 1703 Dihedral : 11.261 82.021 1422 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 25.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 5.05 % Allowed : 28.74 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.23), residues: 1191 helix: 0.41 (0.21), residues: 581 sheet: -0.03 (0.37), residues: 194 loop : -0.97 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 251 TYR 0.173 0.003 TYR A 224 PHE 0.041 0.003 PHE B 378 TRP 0.010 0.001 TRP A 388 HIS 0.015 0.002 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9681) covalent geometry : angle 0.85875 (13128) hydrogen bonds : bond 0.05501 ( 499) hydrogen bonds : angle 5.60592 ( 1551) Misc. bond : bond 0.01655 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8285 (mtmt) REVERT: B 270 PHE cc_start: 0.6824 (t80) cc_final: 0.6506 (t80) REVERT: B 293 MET cc_start: 0.8120 (mmt) cc_final: 0.7080 (ppp) REVERT: B 299 MET cc_start: 0.7112 (tpp) cc_final: 0.6896 (tpt) REVERT: B 330 MET cc_start: 0.7545 (ppp) cc_final: 0.7276 (ppp) REVERT: A 203 MET cc_start: 0.7357 (mpp) cc_final: 0.6734 (mpp) REVERT: A 212 ILE cc_start: 0.8252 (mm) cc_final: 0.7979 (mm) REVERT: A 220 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5458 (pp20) REVERT: A 267 PHE cc_start: 0.6726 (OUTLIER) cc_final: 0.5679 (p90) REVERT: A 308 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7052 (mpt180) REVERT: A 313 MET cc_start: 0.6311 (mtp) cc_final: 0.5457 (mtt) REVERT: A 373 ARG cc_start: 0.7576 (mpt180) cc_final: 0.7066 (mtt180) REVERT: A 425 MET cc_start: 0.9014 (mmm) cc_final: 0.8661 (mmm) REVERT: A 432 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6107 (t80) REVERT: K 115 MET cc_start: 0.8339 (tpp) cc_final: 0.8104 (ptp) REVERT: K 177 ASP cc_start: 0.7816 (t70) cc_final: 0.7502 (t70) REVERT: K 215 GLU cc_start: 0.5383 (OUTLIER) cc_final: 0.5051 (pm20) REVERT: K 367 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6636 (tm-30) outliers start: 52 outliers final: 38 residues processed: 161 average time/residue: 0.1179 time to fit residues: 25.3189 Evaluate side-chains 155 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 367 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 60 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 48 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 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.083504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.068709 restraints weight = 44821.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.070799 restraints weight = 25507.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.072162 restraints weight = 16864.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.073020 restraints weight = 12470.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.073641 restraints weight = 10102.530| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 1.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9691 Z= 0.202 Angle : 0.980 44.035 13128 Z= 0.494 Chirality : 0.047 0.232 1461 Planarity : 0.008 0.105 1703 Dihedral : 10.787 82.741 1415 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 4.56 % Allowed : 29.32 % Favored : 66.12 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.24), residues: 1191 helix: 0.45 (0.21), residues: 573 sheet: -0.02 (0.38), residues: 190 loop : -1.04 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.001 ARG B 251 TYR 0.169 0.003 TYR A 224 PHE 0.046 0.003 PHE B 378 TRP 0.010 0.002 TRP A 388 HIS 0.015 0.002 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 9681) covalent geometry : angle 0.98013 (13128) hydrogen bonds : bond 0.05542 ( 499) hydrogen bonds : angle 5.66302 ( 1551) Misc. bond : bond 0.01739 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2390.27 seconds wall clock time: 42 minutes 11.62 seconds (2531.62 seconds total)